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Sample records for crystal x-ray analysis

  1. Fourier Analysis and Structure Determination--Part III: X-ray Crystal Structure Analysis.

    Science.gov (United States)

    Chesick, John P.

    1989-01-01

    Discussed is single crystal X-ray crystal structure analysis. A common link between the NMR imaging and the traditional X-ray crystal structure analysis is reported. Claims that comparisons aid in the understanding of both techniques. (MVL)

  2. Crystal quality analysis and improvement using x-ray topography

    Science.gov (United States)

    Maj, J. A.; Goetze, K.; Macrander, A. T.; Zhong, Y. C.; Huang, X. R.; Maj, L.

    2008-08-01

    The Topography X-ray Laboratory of the Advanced Photon Source (APS) at Argonne National Laboratory operates as a collaborative effort with APS users to produce high performance crystals for APS X-ray beamline experiments. For many years the topography laboratory has worked closely with an on-site optics shop to help ensure the production of crystals with the highest quality, most stress-free surface finish possible. It has been instrumental in evaluating and refining methods used to produce high quality crystals. Topographical analysis has shown to be an effective method to quantify and determine the distribution of stresses, to help identify methods that would mitigate the stresses and improve the Rocking curve, and to create CCD images of the crystal. This paper describes the topography process and offers methods for reducing crystal stresses in order to substantially improve the crystal optics.

  3. Crystal quality analysis and improvement using x-ray topography.

    Energy Technology Data Exchange (ETDEWEB)

    Maj, J.; Goetze, K.; Macrander, A.; Zhong, Y.; Huang, X.; Maj, L.; Univ. of Chicago

    2008-01-01

    The Topography X-ray Laboratory of the Advanced Photon Source (APS) at Argonne National Laboratory operates as a collaborative effort with APS users to produce high performance crystals for APS X-ray beamline experiments. For many years the topography laboratory has worked closely with an on-site optics shop to help ensure the production of crystals with the highest quality, most stress-free surface finish possible. It has been instrumental in evaluating and refining methods used to produce high quality crystals. Topographical analysis has shown to be an effective method to quantify and determine the distribution of stresses, to help identify methods that would mitigate the stresses and improve the Rocking curve, and to create CCD images of the crystal. This paper describes the topography process and offers methods for reducing crystal stresses in order to substantially improve the crystal optics.

  4. Purification, crystallization and preliminary X-ray analysis of struthiocalcin 1 from ostrich (Struthio camelus) eggshell

    Energy Technology Data Exchange (ETDEWEB)

    Reyes-Grajeda, Juan Pablo [Unidad de Proteómica Médica, Instituto Nacional de Medicina Genómica, Mexico City (Mexico); Marín-García, Liliana [Instituto de Química, Universidad Nacional Autónoma de México (Mexico); Stojanoff, Vivian [Brookhaven National Laboratories, NSLS, Upton, New York (United States); Moreno, Abel, E-mail: carcamo@servidor.unam.mx [Instituto de Química, Universidad Nacional Autónoma de México (Mexico); Unidad de Proteómica Médica, Instituto Nacional de Medicina Genómica, Mexico City (Mexico)

    2007-11-01

    The purification, crystallization and preliminary X-ray diffraction data of the protein struthiocalcin 1 isolated from ostrich eggshell are reported. The purification, crystallization and preliminary X-ray analysis of struthiocalcin 1 (SCA-1), a protein obtained from the intramineral part of ostrich (Struthio camelus) eggshell, is reported.

  5. Rapid X-ray crystal structure analysis in few second measurements using microstrip gas chamber

    CERN Document Server

    Ochi, A; Tanimori, T; Ohashi, Y; Toyokawa, H; Nishi, Y; Nishi, Y; Nagayoshi, T; Koishi, S

    2001-01-01

    X-ray crystal structure analysis using microstrip gas chamber was successfully carried out in a measurement time within a few seconds. The continuous rotation photograph method, in which most of the diffraction peaks can be obtained within one continuous rotation of the sample crystal (without stopping or oscillation), was applied for this measurement. As an example, the structure of a single crystal of ammonium bitartrate (r=1 mm, spherical) was measured. Diffraction spots from the sample, which were sufficient to obtain crystal structure, were successfully obtained by taking only 2 s measurements with a commercially available laboratory X-ray source.

  6. High Resolution Triple Axis X-Ray Diffraction Analysis of II-VI Semiconductor Crystals

    Science.gov (United States)

    Volz, H. M.; Matyi, R. J.

    1999-01-01

    The objective of this research program is to develop methods of structural analysis based on high resolution triple axis X-ray diffractometry (HRTXD) and to carry out detailed studies of defect distributions in crystals grown in both microgravity and ground-based environments. HRTXD represents a modification of the widely used double axis X-ray rocking curve method for the characterization of grown-in defects in nearly perfect crystals. In a double axis rocking curve experiment, the sample is illuminated by a monochromatic X-ray beam and the diffracted intensity is recorded by a fixed, wide-open detector. The intensity diffracted by the sample is then monitored as the sample is rotated through the Bragg reflection condition. The breadth of the peak, which is often reported as the full angular width at half the maximum intensity (FWHM), is used as an indicator of the amount of defects in the sample. This work has shown that high resolution triple axis X-ray diffraction is an effective tool for characterizing the defect structure in semiconductor crystals, particularly at high defect densities. Additionally, the technique is complimentary to X-ray topography for defect characterization in crystals.

  7. X-Ray Diffraction Analysis of NLO Crystals: Traditional Applications and More New Opportunities

    Science.gov (United States)

    Antipin, Mikhail Yu.; Clark, Ronald D.; Nesterov, Vladimir N.

    1998-01-01

    Single crystal X-ray diffraction analysis is one of the more important methods for the molecular and crystal structure determination of matter and therefore it has a great importance in material science including design and engineering of different compounds with non-linear optical (NLO) properties. It was shown in our previous publications that this method provides unique information about molecular structure of NLO compounds, their crystal symmetry and crystal packing arrays, molecular conformation and geometries and many other structural and electronic characteristics that are important for understanding the nature of NLO properties of solids. A very new application of the X-ray diffraction method is related to analysis of the electron density distribution p(r) in crystals and some of its characteristics (atomic and group charges, dipole and higher multipole moments, etc.), that may be obtained directly form the diffraction measurements. In the present work, we will discuss our preliminary low temperature high-resolution X-ray data for the m-nitroaniline (mNA) single crystal (VI). This is one of the "classical" organic NLO materials and electron density distribution analysis in this simple compound has a great scientific interest.

  8. Crystallization and preliminary X-ray diffraction analysis of red clover necrotic mosaic virus

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Stanton L.; Guenther, Richard H.; Sit, Tim L.; Swartz, Paul D.; Meilleur, Flora; Lommel, Steven A.; Rose, Robert B. (NCSU)

    2010-11-12

    Red clover necrotic mosaic virus (RCNMV) is a species that belongs to the Tombusviridae family of plant viruses with a T = 3 icosahedral capsid. RCNMV virions were purified and were crystallized for X-ray analysis using the hanging-drop vapor-diffusion method. Self-rotation functions and systematic absences identified the space group as I23, with two virions in the unit cell. The crystals diffracted to better than 4 {angstrom} resolution but were very radiation-sensitive, causing rapid decay of the high-resolution reflections. The data were processed to 6 {angstrom} in the analysis presented here.

  9. Purification, crystallization and preliminary X-ray analysis of uridine phosphorylase from Salmonella typhimurium.

    Science.gov (United States)

    Dontsova, Mariya V; Savochkina, Yulia A; Gabdoulkhakov, Azat G; Baidakov, Sergey N; Lyashenko, Andrey V; Zolotukhina, Maria; Errais Lopes, Liubov; Garber, Mariya B; Morgunova, Ekaterina Yu; Nikonov, Stanislav V; Mironov, Alexandr S; Ealick, Steven E; Mikhailov, Al 'Bert M

    2004-04-01

    The structural udp gene encoding uridine phosphorylase (UPh) was cloned from the Salmonella typhimurium chromosome and overexpressed in Escherichia coli cells. S. typhimurium UPh (StUPh) was purified to apparent homogeneity and crystallized. The primary structure of StUPh has high homology to the UPh from E. coli, but the enzymes differ substantially in substrate specificity and sensitivity to the polarity of the medium. Single crystals of StUPh were grown using hanging-drop vapor diffusion with PEG 8000 as the precipitant. X-ray diffraction data were collected to 2.9 A resolution. Preliminary analysis of the diffraction data indicated that the crystal belonged to space group P6(1(5)), with unit-cell parameters a = 92.3, c = 267.5 A. The solvent content is 37.7% assuming the presence of one StUPh hexamer per asymmetric unit.

  10. Triethylammonium salt of dimethyl diphenyldithiophosphates: Single crystal X-ray and DFT analysis

    Indian Academy of Sciences (India)

    SANDEEP KUMAR; RUCHI KHAJURIA; MANDEEP KOUR; RAKESH KUMAR; LOVE KARAN RANA; GEETA HUNDAL; VIVEK K GUPTA; RAJNI KANT; SUSHIL K PANDEY

    2016-06-01

    The present work demonstrates the single crystal X-ray and DFT analysis of $ [{(2,4-CH_{3})_{2}C_{6}H_{3}O}_{2}$PS_{2}HNEt_{3}]$ (1) and $ [{(3,4-CH_{3})_{2}$ $C_{6}H_{3}O}_{2}$ $PS_{2}HNEt_{3}]$ (2) along with computational analysis of $ [{(3,5-CH_{3})_{2}C_{6}H_{3}O}_{2} $PS_{2}HNEt_{3}]$ (3) by using density functional theory (DFT) in its hybrid form B3LYP method. Compounds1 and 2 crystallize in the orthorhombic space group Pbca and triclinic space groupP1,respectively andtheir X-ray analysis reveals that phosphorus atom is coordinated to the two S and two O atoms to form tetrahedralgeometry. The structure is stabilized by cation–anion N–H.... S hydrogen bonded interactions. The structuralparameters, vibrational bands and energy gaps of frontier orbitals (HOMO–LUMO) have been calculated.The calculated geometric and spectral results matched the experimental data with good agreement. Theoreticallycalculated frontier molecular orbitals (HOMO–LUMO) and their energies suggest that charge transferoccurs within the compounds.

  11. Crystallization and preliminary X-ray analysis of alginate importer from Sphingomonas sp. A1.

    Science.gov (United States)

    Maruyama, Yukie; Itoh, Takafumi; Nishitani, Yu; Mikami, Bunzo; Hashimoto, Wataru; Murata, Kousaku

    2012-03-01

    Sphingomonas sp. A1 directly incorporates alginate polysaccharides through a 'superchannel' comprising a pit on the cell surface, alginate-binding proteins in the periplasm and an ABC transporter (alginate importer) in the inner membrane. Alginate importer, consisting of four subunits, AlgM1, AlgM2 and two molecules of AlgS, was crystallized in the presence of the binding protein AlgQ2. Preliminary X-ray analysis showed that the crystal diffracted to 3.3 Å resolution and belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 72.5, b = 136.8, c = 273.3 Å, suggesting the presence of one complex in the asymmetric unit.

  12. Crystallization and preliminary X-ray structure analysis of human ribosomal protein L30e.

    Science.gov (United States)

    Kawaguchi, Akiko; Ose, Toyoyuki; Yao, Min; Tanaka, Isao

    2011-12-01

    Many functions have been reported for the eukaryotic ribosomal protein L30e. L30e makes several inter-subunit and intra-subunit interactions with protein or RNA components of the 80S ribosome. Yeast L30e has been shown to bind to its own transcript to autoregulate expression at both the transcriptional and the translational levels. Furthermore, it has been reported that mammalian L30e is a component of the selenocysteine-incorporation machinery by binding to the selenocysteine-insertion sequence on mRNA. As high-resolution crystal structures of mammalian L30e are not available, the purification, crystallization and X-ray structure analysis of human L30e are presented here.

  13. Crystallization and preliminary X-ray diffraction analysis of restriction endonuclease EcoRII

    Science.gov (United States)

    Karpova, E. A.; Meehan, E.; Pusey, M. L.; Chen, L.

    1999-01-01

    Crystals of the restriction endonuclease EcoRII have been obtained by the vapor-diffusion technique in the presence of ammonium sulfate or polyethylene glycol. The best crystals were grown with ammonium sulfate as a precipitant. Crystals with dimensions of up to 0.6 x 0. 6 x 0.6 mm have been observed. The crystals diffract to about 4.0 A resolution at a cryo-temperature of 100 K using a rotating-anode X-ray source and a Rigaku R-AXIS IV imaging-plate detector. The space group has been determined to be either I23 or I2(1)3, with unit-cell parameters a = b = c = 160.3 A, alpha = beta = gamma = 90 degrees. The crystal asymmetric unit contains two protein molecules, and self-rotation function analysis shows a pseudo-twofold symmetry relating the two monomers. Attempts to improve the resolution of crystal diffraction and to search for heavy-atom derivatives are under way.

  14. The purification, crystallization and preliminary X-ray diffraction analysis of dihydrodipicolinate synthase from Clostridium botulinum

    Energy Technology Data Exchange (ETDEWEB)

    Dobson, Renwick C. J., E-mail: rdobson@unimelb.edu.au; Atkinson, Sarah C. [Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010 (Australia); Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, Victoria 3010 (Australia); Gorman, Michael A. [St Vincents Institute, 9 Princes Street, Fitzroy, Victoria 3065 (Australia); Newman, Janet M. [CSIRO Division of Molecular and Health Technologies, 343 Royal Parade, Parkville, Victoria 3052 (Australia); Parker, Michael W. [Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010 (Australia); Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, Victoria 3010 (Australia); St Vincents Institute, 9 Princes Street, Fitzroy, Victoria 3065 (Australia); Perugini, Matthew A. [Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010 (Australia); Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, Victoria 3010 (Australia)

    2008-03-01

    Dihydrodipicolinate synthase (DHDPS), an enzyme in the lysine-biosynthetic pathway, is a promising target for antibiotic development against pathogenic bacteria. Here, the expression, purification, crystallization and preliminary diffraction analysis of DHDPS from C. botulinum are reported. In recent years, dihydrodipicolinate synthase (DHDPS; EC 4.2.1.52) has received considerable attention from both mechanistic and structural viewpoints. This enzyme, which is part of the diaminopimelate pathway leading to lysine, couples (S)-aspartate-β-semialdehyde with pyruvate via a Schiff base to a conserved active-site lysine. In this paper, the expression, purification, crystallization and preliminary X-ray diffraction analysis of DHDPS from Clostridium botulinum, an important bacterial pathogen, are presented. The enzyme was crystallized in a number of forms, predominantly using PEG precipitants, with the best crystal diffracting to beyond 1.9 Å resolution and displaying P4{sub 2}2{sub 1}2 symmetry. The unit-cell parameters were a = b = 92.9, c = 60.4 Å. The crystal volume per protein weight (V{sub M}) was 2.07 Å{sup 3} Da{sup −1}, with an estimated solvent content of 41%. The structure of the enzyme will help guide the design of novel therapeutics against the C. botulinum pathogen.

  15. Crystallization and preliminary X-ray diffraction analysis of human adenovirus

    Energy Technology Data Exchange (ETDEWEB)

    Reddy, V.S.; Natchiar, S.K.; Gritton, L.; Mullen, T.-M.; Stewart, P.L.; Nemerow, G.R. (Scripps); (Vanderbilt)

    2010-07-22

    Replication-defective and conditionally replicating adenovirus (AdV) vectors are currently being utilized in {approx}25% of human gene transfer clinical trials. Unfortunately, progress in vector development has been hindered by a lack of accurate structural information. Here we describe the crystallization and preliminary X-ray diffraction analysis of a HAdV5 vector that displays a short flexible fiber derived from HAdV35. Crystals of Ad35F were grown in 100 mM HEPES pH 7.0, 200 mM Ca(OAc){sub 2}, 14% PEG 550 MME, 15% glycerol in 100 mM Tris-HCl 8.5. Freshly grown crystals diffracted well to 4.5 {angstrom} resolution and weakly to 3.5 {angstrom} at synchrotron sources. HAdV crystals belong to space group P1 with unit cell parameters a = 854.03 {angstrom}, b = 855.17 {angstrom}, c = 865.24 {angstrom}, {alpha} = 119.57{sup o}, {beta} = 91.71{sup o}, {gamma} = 118.08{sup o} with a single particle in the unit cell. Self-rotation and locked-rotation function analysis allowed the determination of the particle orientation. Molecular replacement, density modification and phase-extension procedures are being employed for structure determination.

  16. Crystallization and preliminary X-ray analysis of Chandipura virus glycoprotein G.

    Science.gov (United States)

    Baquero, Eduard; Buonocore, Linda; Rose, John K; Bressanelli, Stéphane; Gaudin, Yves; Albertini, Aurélie A

    2012-09-01

    Fusion in members of the Rhabdoviridae virus family is mediated by the G glycoprotein. At low pH, the G glycoprotein catalyzes fusion between viral and endosomal membranes by undergoing a major conformational change from a pre-fusion trimer to a post-fusion trimer. The structure of the G glycoprotein from vesicular stomatitis virus (VSV G), the prototype of Vesiculovirus, has recently been solved in its trimeric pre-fusion and post-fusion conformations; however, little is known about the structural details of the transition. In this work, a soluble form of the ectodomain of Chandipura virus G glycoprotein (CHAV G(th)) was purified using limited proteolysis of purified virus; this soluble ectodomain was also crystallized. This protein shares 41% amino-acid identity with VSV G and thus its structure could provide further clues about the structural transition of rhabdoviral glycoproteins induced by low pH. Crystals of CHAV G(th) obtained at pH 7.5 diffracted X-rays to 3.1 Å resolution. These crystals belonged to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 150.3, b = 228.2, c = 78.8 Å. Preliminary analysis of the data based on the space group and the self-rotation function indicated that there was no trimeric association of the protomers. This unusual oligomeric status could result from the presence of fusion intermediates in the crystal.

  17. Cloning, expression, crystallization and preliminary X-ray data analysis of norcoclaurine synthase from Thalictrum flavum

    Energy Technology Data Exchange (ETDEWEB)

    Pasquo, Alessandra [ENEA Casaccia Research Centre, Dipartimento BIOTEC, Sezione Genetica e Genomica Vegetale, PO Box 2400, I-00100 Rome (Italy); Bonamore, Alessandra; Franceschini, Stefano; Macone, Alberto; Boffi, Alberto; Ilari, Andrea, E-mail: andrea.ilari@uniroma1.it [Istituto di Biologia e Patologia Molecolari, CNR (IBPM) and Department Of Biochemical Sciences, University of Roma ‘La Sapienza’, Piazza Aldo Moro 5, 00179 Roma (Italy); ENEA Casaccia Research Centre, Dipartimento BIOTEC, Sezione Genetica e Genomica Vegetale, PO Box 2400, I-00100 Rome (Italy)

    2008-04-01

    The cloning, expression, crystallization and preliminary X-ray data analysis of norcoclaurine synthase from T. flavum, a protein which catalyzes the first committed step in the biosynthesis of benzylisoquinoline alkaloids, are reported. Norcoclaurine synthase (NCS) catalyzes the condensation of 3,4-dihydroxyphenylethylamine (dopamine) and 4-hydroxyphenylacetaldehyde (4-HPAA) as the first committed step in the biosynthesis of benzylisoquinoline alkaloids in plants. The protein was cloned, expressed and purified. Crystals were obtained at 294 K by the hanging-drop vapour-diffusion method using ammonium sulfate and sodium chloride as precipitant agents and diffract to better than 3.0 Å resolution using a synchrotron-radiation source. The crystals belong to the trigonal space group P3{sub 1}21, with unit-cell parameters a = b = 86.31, c = 118.36 Å. A selenomethionine derivative was overexpressed, purified and crystallized in the same space group. A complete MAD data set was collected at 2.7 Å resolution. The model is under construction.

  18. Crystallization and X-ray diffraction analysis of recombinant Coprinus cinereus peroxidase.

    Science.gov (United States)

    Petersen, J F; Tams, J W; Vind, J; Svensson, A; Dalbøge, H; Welinder, K G; Larsen, S

    1993-08-01

    Crystals suitable for an X-ray diffraction investigation have been obtained of recombinant Coprinus cinereus peroxidase expressed in Aspergillus oryzae. The crystals were grown by the hanging drop method with polyethylene glycol 6000 as the precipitant. A pH range from 6.2 to 8.0 and CaCl2 or MgCl2 present at a concentration of 0.35 M were essential for the crystal growth. A metastable monoclinic modification can be obtained under certain conditions, and with variations in temperature they are transformed into a stable orthorhombic modification. With CaCl2 as the additive, the unit cell dimensions were a = 74.9 A, b = 76.8 A and c = 128.2 A. With two peroxidase molecules per asymmetric unit, the solvent content is 49% (v/v). In the diffraction pattern, the reflections Okl are systematically very weak for k = 2n + 1. Combined with an analysis of the Patterson function, this showed that the two independent molecules are related by the pseudotranslational symmetry 0.29a + 0.5b. The possible space groups are P2(1)2(1)2(1) or P2(1)22(1) because of this pseudosymmetry. The crystals diffract to a resolution of 2.9 A.

  19. Ultrasmall-angle X-ray scattering analysis of photonic crystal structure

    NARCIS (Netherlands)

    Abramova, V.V.; Sinitskii, A.S.; Grigoryeva, N.A.; Grigoriev, S.V.; Belov, D.V.; Petukhov, A.V.; Mistonov, A.A.; Vasilieva, A.V.; Tretyakov, Y.D.

    2009-01-01

    The results of an ultrasmall angle X ray scattering study of iron(III) oxide inverse opal thin films are presented. The photonic crystals examined are shown to have fcc structure with amount of stacking faults varying among the samples. The method used in this study makes it possible to easily disti

  20. Crystallization and Preliminary X-ray Diffraction Analysis of Salmonella typhi PilS

    Energy Technology Data Exchange (ETDEWEB)

    Balakrishna,A.; Tan, Y.; Mok, H.; Saxena, A.; Swaminathan, K.

    2006-01-01

    The structure determination of PilS, a type IV pilin, by X-ray crystallography is reported. The recombinant protein from Salmonella typhi was overexpressed, purified and crystallized. The crystals belong to space group P2{sub 1}2{sub 1}2, with unit-cell parameters a = 77.88, b = 114.53, c = 31.75 {angstrom}. The selenomethionine derivative of the PilS protein was overexpressed, purified and crystallized in the same space group. Data sets have been collected to 2.1 {angstrom} resolution from the selenomethionine-derivative crystal using synchrotron radiation for multiwavelength anomalous dispersion (MAD) phasing.

  1. Purification, crystallization and preliminary X-ray analysis of the membrane-bound [NiFe] hydrogenase from Allochromatium vinosum

    Energy Technology Data Exchange (ETDEWEB)

    Kellers, Petra; Ogata, Hideaki; Lubitz, Wolfgang, E-mail: lubitz@mpi-muelheim.mpg.de [Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr (Germany)

    2008-08-01

    This article describes the first successful crystallization of a membrane-bound [NiFe] hydrogenase isolated from a photosynthetic organism (A. vinosum). The crystals obtained produced diffraction patterns up to 2.5 Å resolution. The membrane-bound [NiFe] hydrogenase is a unique metalloprotein that is able to catalyze the reversible oxidation of hydrogen to protons and electrons during a complex reaction cycle. The [NiFe] hydrogenase was isolated from the photosynthetic purple sulfur bacterium Allochromatium vinosum and its crystallization and preliminary X-ray analysis are reported. It was crystallized by the hanging-drop vapour-diffusion method using sodium citrate and imidazole as crystallization agents. The crystals belong to space group P2{sub 1}2{sub 1}2, with unit-cell parameters a = 205.00, b = 217.42, c = 120.44 Å. X-ray diffraction data have been collected to 2.5 Å resolution.

  2. Instrument and method for X-ray diffraction, fluorescence, and crystal texture analysis without sample preparation

    Science.gov (United States)

    Gendreau, Keith (Inventor); Martins, Jose Vanderlei (Inventor); Arzoumanian, Zaven (Inventor)

    2010-01-01

    An X-ray diffraction and X-ray fluorescence instrument for analyzing samples having no sample preparation includes a X-ray source configured to output a collimated X-ray beam comprising a continuum spectrum of X-rays to a predetermined coordinate and a photon-counting X-ray imaging spectrometer disposed to receive X-rays output from an unprepared sample disposed at the predetermined coordinate upon exposure of the unprepared sample to the collimated X-ray beam. The X-ray source and the photon-counting X-ray imaging spectrometer are arranged in a reflection geometry relative to the predetermined coordinate.

  3. Crystallization of prostaglandin-H synthase for X-ray structure analysis

    Energy Technology Data Exchange (ETDEWEB)

    Jahnke, K.; Degen, G.H.; Buehner, M. (Univ. of Wuerzburg (West Germany))

    1990-08-01

    Prostaglandin-H (PGH) synthase from ram seminal vesicles is a dimeric integral membrane protein of molecular weight 140 kDa. PGH synthase is a key enzyme in the biosynthesis of prostaglandins, has cyclooxygenase and peroxidase activities, and contains heme as a coenzyme. In the peroxidation step of its reaction, PGH synthase can use xenobiotics as co-substrates and can catalyze the metabolic activation of carcinogens such as diethylstilbestrol. To gain a detailed understanding of the inner workings of PGH synthase, the authors are investigating its three-dimensional structure by X-ray crystallography. A purification procedure was established that yields stable homogeneous PGH synthase that is at least 80% holoenzyme. Manipulation of these crystals is very difficult due to the small volume of the growth phase. The crystals dissolved rapidly in all aqueous media into which they were transferred for mounting in X-ray capillaries. Therefore, the authors have not yet been able to demonstrate their true X-ray scattering power. A crystal provisionally dry mounted diffracted to about 8 {angstrom} resolution.

  4. Crystallization and preliminary X-ray diffraction analysis of maize aldose reductase

    Energy Technology Data Exchange (ETDEWEB)

    Kiyota, Eduardo [Laboratório de Biologia Estrutural, Instituto de Química, Universidade Estadual de Campinas, CP 6154, 13083-970 Campinas-SP (Brazil); Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas-SP (Brazil); Sousa, Sylvia Morais de [Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas-SP (Brazil); Santos, Marcelo Leite dos; Costa Lima, Aline da [Laboratório de Biologia Estrutural, Instituto de Química, Universidade Estadual de Campinas, CP 6154, 13083-970 Campinas-SP (Brazil); Menossi, Marcelo [Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas-SP (Brazil); Yunes, José Andrés [Laboratório de Biologia Molecular, Centro Infantil Boldrini, Campinas-SP (Brazil); Aparicio, Ricardo, E-mail: aparicio@iqm.unicamp.br [Laboratório de Biologia Estrutural, Instituto de Química, Universidade Estadual de Campinas, CP 6154, 13083-970 Campinas-SP (Brazil)

    2007-11-01

    Preliminary X-ray diffraction studies of apo maize aldose reductase at 2.0 Å resolution are reported. Maize aldose reductase (AR) is a member of the aldo-keto reductase superfamily. In contrast to human AR, maize AR seems to prefer the conversion of sorbitol into glucose. The apoenzyme was crystallized in space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 47.2, b = 54.5, c = 100.6 Å and one molecule in the asymmetric unit. Synchrotron X-ray diffraction data were collected and a final resolution limit of 2.0 Å was obtained after data reduction. Phasing was carried out by an automated molecular-replacement procedure and structural refinement is currently in progress. The refined structure is expected to shed light on the functional/enzymatic mechanism and the unusual activities of maize AR.

  5. Crystallization and preliminary X-ray analysis of CTP:phosphoethanolamine cytidylyltransferase (ECT) from Saccharomyces cerevisiae

    Energy Technology Data Exchange (ETDEWEB)

    Ohtsuka, Jun; Nagata, Koji; Lee, Woo Cheol [Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657 (Japan); Ono, Yusuke; Fukuda, Ryouichi; Ohta, Akinori [Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657 (Japan); Tanokura, Masaru, E-mail: amtanok@mail.ecc.u-tokyo.ac.jp [Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657 (Japan)

    2006-10-01

    CTP:phosphoethanolamine cytidylyltransferase from S. cerevisiae has been expressed, purified and crystallized. CTP:phosphoethanolamine cytidylyltransferase (ECT) is the enzyme that catalyzes the conversion of phosphoethanolamine to CDP-ethanolamine in the phosphatidylethanolamine-biosynthetic pathway (Kennedy pathway). ECT from Saccharomyces cerevisiae was crystallized by the sitting-drop vapour-diffusion method using PEG 4000 as precipitant. The crystals diffracted X-rays from a synchrotron-radiation source to 1.88 Å resolution. The space group was assigned as primitive tetragonal, P4{sub 1}2{sub 1}2 or P4{sub 3}2{sub 1}2, with unit-cell parameters a = b = 66.3, c = 150.8 Å. The crystals contain one ECT molecule in the asymmetric unit (V{sub M} = 2.2 Å{sup 3} Da{sup −1}), with a solvent content of 43%.

  6. Overexpression, crystallization and preliminary X-ray crystallographic analysis of phosphopantetheine adenylyltransferase from Enterococcus faecalis

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Ji Yong; Lee, Hyung Ho; Yoon, Hye Jin; Kim, Hyoun Sook; Suh, Se Won, E-mail: sewonsuh@snu.ac.kr [Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742 (Korea, Republic of)

    2006-11-01

    Phosphopantetheine adenylyltransferase from En. faecalis was crystallized and X-ray diffraction data were collected to 2.70 Å resolution. Phosphopantetheine adenylyltransferase, an essential enzyme in the coenzyme A biosynthetic pathway, catalyzes the reversible transfer of an adenylyl group from ATP to 4′-phosphopantetheine, yielding 3′-dephospho-CoA and pyrophosphate. Enterococcus faecalis PPAT has been overexpressed in Escherichia coli as a fusion with a C-terminal purification tag and crystallized at 297 K using a reservoir solution consisting of 0.1 M sodium HEPES pH 7.5, 0.8 M sodium dihydrogen phosphate and 0.8 M potassium dihydrogen phosphate. X-ray diffraction data were collected to 2.70 Å at 100 K. The crystals belong to the primitive tetragonal space group P4{sub 1} (or P4{sub 3}), with unit-cell parameters a = b = 160.81, c = 225.68 Å. Four copies of the hexameric molecule are likely to be present in the asymmetric unit, giving a crystal volume per protein weight (V{sub M}) of 3.08 Å{sup 3} Da{sup −1} and a solvent content of 60.1%.

  7. Crystallization and preliminary X-ray diffraction analysis of apolipoprotein E-containing lipoprotein particles

    Energy Technology Data Exchange (ETDEWEB)

    Newhouse, Yvonne [Gladstone Institutes of Cardiovascular and Neurological Disease, University of California, San Francisco, CA 94158 (United States); Peters-Libeu, Clare [Gladstone Institutes of Cardiovascular and Neurological Disease, University of California, San Francisco, CA 94158 (United States); Cardiovascular Research Institute, University of California, San Francisco, CA 94158 (United States); Weisgraber, Karl H., E-mail: kweisgraber@gladstone.ucsf.edu [Gladstone Institutes of Cardiovascular and Neurological Disease, University of California, San Francisco, CA 94158 (United States); Cardiovascular Research Institute, University of California, San Francisco, CA 94158 (United States); Department of Pathology, University of California, San Francisco, CA 94158 (United States)

    2005-11-01

    Further understanding of the structure and function of plasma apolipoproteins requires the determination of their high-resolution structures when complexed with lipids. In these studies, the production of homogeneous, biologically active lipoprotein particles of apolipoprotein E complexed with dipalmitoylphosphatidylcholine and their crystallization and X-ray diffraction are demonstrated. High-resolution structural information is available for several soluble plasma apolipoproteins (apos) in a lipid-free state. However, this information provides limited insight into structure–function relationships, as this class of proteins primarily performs its functions of lipid transport and modulation of lipid metabolism in a lipid-bound state on lipoprotein particles. Here, the possibility of generating homogeneous lipoprotein particles that could be crystallized was explored, opening the possibility of obtaining high-resolution structural information by X-ray crystallography. To test this possibility, apoE4 complexed with the phospholipid dipalmitoylphosphatidylcholine was chosen. Uniform particles containing 50% lipid and 50% apoE4 were obtained and crystallized using the hanging-drop method. Two crystal forms diffract to beyond 8 Å resolution.

  8. Crystallization and preliminary X-ray diffraction analysis of recombinant hepatitis E virus-like particle

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Che-Yen [Molecular and Cellular Biology, University of California, Davis, CA 95616 (United States); Karolinska Institute Structural Virology, F68 Karolinska University Hospital, SE-14186 Stockholm (Sweden); Institute of Public Health, National Yang-Ming University, 112 Taipei,Taiwan (China); Miyazaki, Naoyuki [Molecular and Cellular Biology, University of California, Davis, CA 95616 (United States); Karolinska Institute Structural Virology, F68 Karolinska University Hospital, SE-14186 Stockholm (Sweden); Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Yamashita, Tetsuo [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Institute for Microbial Diseases, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Higashiura, Akifumi; Nakagawa, Atsushi [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Li, Tian-Cheng; Takeda, Naokazu [Department of Virology II, National Institute of Infectious Diseases, Tokyo (Japan); Xing, Li [Molecular and Cellular Biology, University of California, Davis, CA 95616 (United States); Karolinska Institute Structural Virology, F68 Karolinska University Hospital, SE-14186 Stockholm (Sweden); Hjalmarsson, Erik; Friberg, Claes [Crystal Research AB, 22370 Lund (Sweden); Liou, Der-Ming [Institute of Public Health, National Yang-Ming University, 112 Taipei,Taiwan (China); Sung, Yen-Jen [Institute of Public Health, National Yang-Ming University, 112 Taipei,Taiwan (China); Institute of Anatomy and Cell Biology, National Yang-Ming University, 112 Taipei,Taiwan (China); Tsukihara, Tomitake [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Matsuura, Yoshiharu [Institute for Microbial Diseases, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Miyamura, Tatsuo [Department of Virology II, National Institute of Infectious Diseases, Tokyo (Japan); Cheng, R. Holland, E-mail: rhch@ucdavis.edu [Molecular and Cellular Biology, University of California, Davis, CA 95616 (United States); Karolinska Institute Structural Virology, F68 Karolinska University Hospital, SE-14186 Stockholm (Sweden)

    2008-04-01

    A recombinant virus-like particle that is a potential oral hepatitis E vaccine was crystallized. Diffraction data were collected to 8.3 Å resolution and the X-ray structure was phased with the aid of a low-resolution density map determined using cryo-electron microscopy data. Hepatitis E virus (HEV) accounts for the majority of enterically transmitted hepatitis infections worldwide. Currently, there is no specific treatment for or vaccine against HEV. The major structural protein is derived from open reading frame (ORF) 2 of the viral genome. A potential oral vaccine is provided by the virus-like particles formed by a protein construct of partial ORF3 protein (residue 70–123) fused to the N-terminus of the ORF2 protein (residues 112–608). Single crystals obtained by the hanging-drop vapour-diffusion method at 293 K diffract X-rays to 8.3 Å resolution. The crystals belong to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 337, b = 343, c = 346 Å, α = β = γ = 90°, and contain one particle per asymmetric unit.

  9. Au36(SPh)24 nanomolecules: X-ray crystal structure, optical spectroscopy, electrochemistry, and theoretical analysis.

    Science.gov (United States)

    Nimmala, Praneeth Reddy; Knoppe, Stefan; Jupally, Vijay Reddy; Delcamp, Jared H; Aikens, Christine M; Dass, Amala

    2014-12-11

    The physicochemical properties of gold:thiolate nanomolecules depend on their crystal structure and the capping ligands. The effects of protecting ligands on the crystal structure of the nanomolecules are of high interest in this area of research. Here we report the crystal structure of an all aromatic thiophenolate-capped Au36(SPh)24 nanomolecule, which has a face-centered cubic (fcc) core similar to other nanomolecules such as Au36(SPh-tBu)24 and Au36(SC5H9)24 with the same number of gold atoms and ligands. The results support the idea that a stable core remains intact even when the capping ligand is varied. We also correct our earlier assignment of "Au36(SPh)23" which was determined based on MALDI mass spectrometry which is more prone to fragmentation than ESI mass spectrometry. We show that ESI mass spectrometry gives the correct assignment of Au36(SPh)24, supporting the X-ray crystal structure. The electronic structure of the title compound was computed at different levels of theory (PBE, LDA, and LB94) using the coordinates extracted from the single crystal X-ray diffraction data. The optical and electrochemical properties were determined from experimental data using UV-vis spectroscopy, cyclic voltammetry, and differential pulse voltammetry. Au36(SPh)24 shows a broad electrochemical gap near 2 V, a desirable optical gap of ∼1.75 eV for dye-sensitized solar cell applications, as well as appropriately positioned electrochemical potentials for many electrocatalytic reactions.

  10. Crystallization and preliminary X-ray analysis of glutathione transferases from cyanobacteria

    Energy Technology Data Exchange (ETDEWEB)

    Feil, Susanne C.; Tang, Julian; Hansen, Guido; Gorman, Michael A.; Wiktelius, Eric; Stenberg, Gun; Parker, Michael W.; (SVIMR-A); (Uppsala)

    2009-05-08

    Glutathione S-transferases (GSTs) are a group of multifunctional enzymes that are found in animals, plants and microorganisms. Their primary function is to remove toxins derived from exogenous sources or the products of metabolism from the cell. Mammalian GSTs have been extensively studied, in contrast to bacterial GSTs which have received relatively scant attention. A new class of GSTs called Chi has recently been identified in cyanobacteria. Chi GSTs exhibit a high glutathionylation activity towards isothiocyanates, compounds that are normally found in plants. Here, the crystallization of two GSTs are presented: TeGST produced by Thermosynechococcus elongates BP-1 and SeGST from Synechococcus elongates PCC 6301. Both enzymes formed crystals that diffracted to high resolution and appeared to be suitable for further X-ray diffraction studies. The structures of these GSTs may shed further light on the evolution of GST catalytic activity and in particular why these enzymes possess catalytic activity towards plant antimicrobial compounds.

  11. Crystallization and preliminary X-ray crystallographic analysis of zebrafish prototype galectin Drgal1-L2.

    Science.gov (United States)

    Scott, Stacy A; Cozier, Matthew O; Dubar, Pauline D I; Ramakrishna, Manasa; Scott, Ken; Blanchard, Helen

    2010-12-01

    Zebrafish (Danio rerio) are an important developmental and embryological model given the optical clarity of the embryos and larvae, which permits real-time viewing of developing pathologies. More recently, a broader scope for these vertebrates to model a range of human diseases, including some cancers, has been indicated. Zebrafish Drgal1-L2 has been identified as an orthologue of mammalian galectin-1, which is is a carbohydrate-binding protein that exhibits β-galactoside-binding specificity and which is overexpressed by many aggressive human cancers. This study describes the cloning, expression in Escherichia coli, purification and crystallization of recombinant Drgal1-L2 protein in the presence of lactose (ligand). X-ray diffraction data from these novel crystals of zebrafish Drgal1-L2 were collected to a resolution of 1.5 Å using a synchrotron-radiation source, enabling their characterization.

  12. Expression, purification, crystallization and preliminary X-ray crystallographic analysis of Zucchini from Drosophila melanogaster.

    Science.gov (United States)

    Fukuhara, Satoshi; Nishimasu, Hiroshi; Bonnefond, Luc; Matsumoto, Naoki; Ishitani, Ryuichiro; Nureki, Osamu

    2012-11-01

    PIWI-interacting RNAs (piRNAs) bind PIWI proteins and silence transposons to maintain the genomic integrity of germ cells. Zucchini (Zuc), a phospholipase D superfamily member, is conserved among animals and is implicated in piRNA biogenesis. However, the underlying mechanism by which Zuc participates in piRNA biogenesis remains elusive. Drosophila melanogaster Zuc (DmZuc) was expressed in Escherichia coli, purified and crystallized. X-ray diffraction data were collected to 1.75 Å resolution. The crystal belonged to space group P2(1), with unit-cell parameters a=55.0, b=71.2, c=56.3 Å, β=107.9°.

  13. Crystallization and preliminary X-ray diffraction analysis of HML, a lectin from the red marine alga Hypnea musciformis

    Energy Technology Data Exchange (ETDEWEB)

    Nagano, Celso S.; Gallego del Sol, Francisca [Instituto de Biomedicina de Valencia, CSIC, Valencia (Spain); Cavada, Benildo S.; Nascimento, Kyria Santiago Do [Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, CE 60451-970 (Brazil); Nunes, Eudismar Vale; Sampaio, Alexandre H. [Laboratorio de Bioquímica Marinha, Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Fortaleza, CE 60451-970 (Brazil); Calvete, Juan J., E-mail: jcalvete@ibv.csic.es [Instituto de Biomedicina de Valencia, CSIC, Valencia (Spain)

    2005-11-01

    The crystallization and preliminary X-ray diffraction analysis of a red marine alga lectin isolated from H. musciformis is reported. HML, a lectin from the red marine alga Hypnea musciformis, defines a novel lectin family. Orthorhombic crystals of HML belonging to space group P2{sub 1}2{sub 1}2{sub 1} grew within three weeks at 293 K using the hanging-drop vapour-diffusion method. A complete data set was collected at 2.4 Å resolution. HML is the first marine alga lectin to be crystallized.

  14. Crystallization and X-ray diffraction analysis of human CLEC-2

    Energy Technology Data Exchange (ETDEWEB)

    Watson, Aleksandra A.; O’Callaghan, Christopher A., E-mail: chrisoc@ccmp.ox.ac.uk [Henry Wellcome Building of Molecular Physiology, University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom)

    2005-12-01

    Recombinant human CLEC-2 was crystallized in the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1} and X-ray diffraction data were collected to 2.0 Å. The human C-type lectin-like protein CLEC-2 has recently been shown to be expressed on the surface of platelets and to function as a receptor for the snake-venom protein rhodocytin. The C-type lectin-like domain (CTLD) of CLEC-2 was expressed in Escherichia coli, refolded and purified. Crystals of this recombinant CLEC-2 were grown by sitting-drop vapour diffusion using polyethylene glycol (PEG) 6000 as a precipitant. After optimization, crystals were grown which diffracted to 2.0 Å using in-house radiation (λ = 1.5418 Å). These crystals belonged to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 35.407, b = 55.143, c = 56.078 Å. The presence of one molecule per asymmetric unit is consistent with a crystal volume per unit weight (V{sub M}) of 1.82 Å{sup 3} Da{sup −1} and a solvent content of 32.6%. These results suggest that crystals producing diffraction of this quality will be suitable for the structural determination of human CLEC-2.

  15. Crystallization and preliminary X-ray crystallographic analysis of yeast NAD{sup +}-specific isocitrate dehydrogenase

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Gang [Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229-3900 (United States); Taylor, Alexander B. [Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229-3900 (United States); X-ray Crystallography Core Laboratory, University of Texas Health Science Center, San Antonio, TX 78229-3900 (United States); McAlister-Henn, Lee [Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229-3900 (United States); Hart, P. John, E-mail: pjhart@biochem.uthscsa.edu [Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229-3900 (United States); X-ray Crystallography Core Laboratory, University of Texas Health Science Center, San Antonio, TX 78229-3900 (United States)

    2005-05-01

    Yeast NAD{sup +}-isocitrate dehydrogenase has been purified and crystallized using sodium citrate, a competitive inhibitor of the enzyme, as a precipitant. Preliminary X-ray analyses indicate the molecular boundaries of the molecule and large continuous solvent channels in the crystal. NAD{sup +}-specific isocitrate dehydrogenase (IDH; EC 1.1.1.41) is a complex allosterically regulated enzyme in the tricarboxylic acid cycle. Yeast IDH is believed to be an octamer containing four catalytic IDH2 and four regulatory IDH1 subunits. Crystals of yeast IDH have been obtained and optimized using sodium citrate, a competitive inhibitor of the enzyme, as the precipitating agent. The crystals belong to space group R3, with unit-cell parameters a = 302.0, c = 112.1 Å. Diffraction data were collected to 2.9 Å from a native crystal and to 4.0 Å using multiwavelength anomalous diffraction (MAD) methods from an osmium derivative. Initial electron-density maps reveal large solvent channels and the molecular boundaries of the allosteric IDH multimer.

  16. Non-destructive analysis of didymium and praseodymium molybdate crystals using energy dispersive X-ray fluorescence technique

    Science.gov (United States)

    Bhat, C. K.; Joseph, Daisy; Pandita, Sanjay; Kotru, P. N.

    2016-08-01

    Analysis of didymium (Di) and praseodymium molybdate crystals were carried out using energy dispersive X-ray fluorescence (EDXRF). The assigned empirical chemical formulae of the composites were tested and verified by the EDXRF technique by estimating experimental major elemental concentration ratios. On the Basis of these ratios, the established formulae for some of the composite materials have been verified and suggestions made for their refinement. Non-destructive technique used in this analysis enables to retain the original crystal samples and makes rapid simultaneous scan of major elements such as La, Pr, Ned and Mo as well as impurities such as Ce. Absence of samarium(Sm) in the spectrum during analysis of didymium molybdate crystals indicated an incomplete growth of mixed rare earth single crystal. These crystals (e.g.,Di) are shown to be of modified stoichiometry with Ce as trace impurity.

  17. Crystallization and preliminary X-ray analysis of the Plasmodium falciparum apicoplast DNA polymerase

    Science.gov (United States)

    Milton, Morgan E.; Choe, Jun-yong; Honzatko, Richard B.; Nelson, Scott W.

    2015-01-01

    Infection by the parasite Plasmodium falciparum is the leading cause of malaria in humans. The parasite has a unique and essential plastid-like organelle called the apicoplast. The apicoplast contains a genome that undergoes replication and repair through the action of a replicative polymerase (apPOL). apPOL has no direct orthologs in mammalian polymerases and is therefore an attractive antimalarial drug target. No structural information exists for apPOL, and the Klenow fragment of Escherichia coli DNA polymerase I, which is its closest structural homolog, shares only 28% sequence identity. Here, conditions for the crystallization of and preliminary X-ray diffraction data from crystals of P. falciparum apPOL are reported. Data complete to 3.5 Å resolution were collected from a single crystal (2 × 2 × 5 µm) using a 5 µm beam. The space group P6522 (unit-cell parameters a = b = 141.8, c = 149.7 Å, α = β = 90, γ = 120°) was confirmed by molecular replacement. Refinement is in progress. PMID:25760711

  18. Purification, crystallization and preliminary X-ray diffraction analysis of water-soluble chlorophyll-binding protein from Chenopodium album

    Energy Technology Data Exchange (ETDEWEB)

    Ohtsuki, Takayuki [Department of Bimolecular Science, Faculty of Science, Toho University, Miyama 2-2-1, Funabashi, Chiba 274-8510 (Japan); Ohshima, Shigeru [Department of Environmental Science, Faculty of Science, Toho University, Miyama 2-2-1, Funabashi, Chiba 274-8510 (Japan); Uchida, Akira, E-mail: auchida@biomol.sci.toho-u.ac.jp [Department of Bimolecular Science, Faculty of Science, Toho University, Miyama 2-2-1, Funabashi, Chiba 274-8510 (Japan)

    2007-09-01

    A water-soluble chlorophyll-binding protein with photoconvertibility from C. album was extracted, purified and crystallized in a darkroom. The crystal diffracted to around 2.0 Å resolution. A water-soluble chlorophyll-binding protein (WSCP) with photoconvertibility from Chenopodium album was extracted, purified and crystallized in a darkroom. Green crystals suitable for data collection appeared in about 10 d. A native data set was collected to 2.0 Å resolution at 100 K. The space group of the crystal was determined to be orthorhombic I222 or I2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 48.13, b = 60.59, c = 107.21 Å. Preliminary analysis of the X-ray data indicated that there is one molecule per asymmetric unit.

  19. X-ray analysis of mechanical and thermal effects induced by femtosecond laser treatment of aluminum single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Valette, S. [Laboratoire Traitement du Signal et Instrumentation, Universite Jean Monnet, UMR CNRS 5516, 10 rue Barrouin 42000 Saint-Etienne (France)]. E-mail: stephane.valette@ec-lyon.fr; Le Harzic, R. [Laboratoire Traitement du Signal et Instrumentation, Universite Jean Monnet, UMR CNRS 5516, 10 rue Barrouin 42000 Saint-Etienne (France); Audouard, E. [Laboratoire Traitement du Signal et Instrumentation, Universite Jean Monnet, UMR CNRS 5516, 10 rue Barrouin 42000 Saint-Etienne (France); Huot, N. [Laboratoire Traitement du Signal et Instrumentation, Universite Jean Monnet, UMR CNRS 5516, 10 rue Barrouin 42000 Saint-Etienne (France); Fillit, R. [Ecole Nationale Superieure des Mines de Saint-Etienne, 158 Cours Fauriel, 42023 Saint-Etienne Cedex 2 (France); Fortunier, R. [Ecole Nationale Superieure des Mines de Saint-Etienne, 158 Cours Fauriel, 42023 Saint-Etienne Cedex 2 (France)

    2006-04-30

    Surface marking of aluminum single crystal is performed with femtosecond laser pulses. X-ray analysis allows to measure thermal and mechanical effects induced by the femtosecond laser pulses. These effects are estimated by comparing the pole figures (crystallinity) and the broadening of the diffraction peaks (mechanical contribution) before and after the laser irradiation. The results show that the femtosecond laser treatment ensures a re-crystallization of the structure and the presence of mechanical residual stresses. The analysis of the pole figures provides the sign of a re-crystallization on smaller volumes compared to initial ones. After the laser irradiation, the crystallization is perfectly oriented like the (1 1 0) orientation of the massive sample. Moreover, following the laser treatment, we show that the crystallographic structure is purer than the initial one. We also prove that the laser effect is persistent on a typical scale of 10 {mu}m beyond the surface.

  20. Purification, crystallization and preliminary X-ray crystallographic analysis of rice bifunctional α-amylase/subtilisin inhibitor from Oryza sativa

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Yi-Hung [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Peng, Wen-Yan [Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsinchu 30013,Taiwan (China); Huang, Yen-Chieh [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Guan, Hong-Hsiang; Hsieh, Ying-Cheng [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsinchu 30013,Taiwan (China); Liu, Ming-Yih [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Chang, Tschining [Department of Hospitality Management, Nan Jeon Institute of Technology, Yen-Shui, Tainan 73746,Taiwan (China); Chen, Chun-Jung, E-mail: cjchen@nsrrc.org.tw [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Department of Physics, National Tsing-Hua University, Hsinchu 30013,Taiwan (China)

    2006-08-01

    The crystallization of rice α-amylase/subtilisin bifunctional inhibitor is reported. Rice bifunctional α-amylase/subtilisin inhibitor (RASI) can inhibit both α-amylase from larvae of the red flour beetle (Tribolium castaneum) and subtilisin from Bacillus subtilis. The synthesis of RASI is up-regulated during the late milky stage in developing seeds. The 8.9 kDa molecular-weight RASI from rice has been crystallized using the hanging-drop vapour-diffusion method. According to 1.81 Å resolution X-ray diffraction data from rice RASI crystals, the crystal belongs to space group P2{sub 1}2{sub 1}2, with unit-cell parameters a = 79.99, b = 62.95, c = 66.70 Å. Preliminary analysis indicates two RASI molecules in an asymmetric unit with a solvent content of 44%.

  1. Purification, crystallization and preliminary X-ray crystallographic analysis of branched-chain aminotransferase from Deinococcus radiodurans

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Chung-Der; Huang, Tien-Feng [Department of Physics, National Tsing-Hua University, Hsinchu 30013,Taiwan (China); Lin, Chih-Hao [Institute of Biological Chemistry, National Taiwan University, Taipei 110,Taiwan (China); Guan, Hong-Hsiang; Hsieh, Yin-Cheng [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsinchu 30013,Taiwan (China); Lin, Yi-Hung; Huang, Yen-Chieh; Liu, Ming-Yih [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Chang, Wen-Chang, E-mail: wchang@ntu.edu.tw [Institute of Biological Chemistry, National Taiwan University, Taipei 110,Taiwan (China); Chen, Chun-Jung, E-mail: wchang@ntu.edu.tw [Department of Physics, National Tsing-Hua University, Hsinchu 30013,Taiwan (China); Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China)

    2007-06-01

    The crystallization of branched-chain aminotransferase from D. radiodurans is described. The branched-chain amino-acid aminotransferase (BCAT), which requires pyridoxal 5′-phosphate (PLP) as a cofactor, is a key enzyme in the biosynthetic pathway of the hydrophobic amino acids leucine, isoleucine and valine. DrBCAT from Deinococcus radiodurans, which has a molecular weight of 40.9 kDa, was crystallized using the hanging-drop vapour-diffusion method. According to X-ray diffraction data to 2.50 Å resolution from a DrBCAT crystal, the crystal belongs to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 56.37, b = 90.70, c = 155.47 Å. Preliminary analysis indicates the presence of two DrBCAT molecules in the asymmetric unit, with a solvent content of 47.52%.

  2. Expression, purification, crystallization and preliminary X-ray analysis of the cathelicidin motif of the protegrin-3 precursor.

    Science.gov (United States)

    Sanchez, J F; Hoh, F; Strub, M P; Strub, J M; Van Dorsselaer, A; Lehrer, R; Ganz, T; Chavanieu, A; Calas, B; Dumas, C; Aumelas, A

    2001-11-01

    Numerous precursors of antibacterial peptides with unrelated sequences share a similar prosequence which belongs to the cathelicidin family of proteins. The three-dimensional structure of this cathelicidin motif, which contains two disulfide bonds, has not yet been reported. The cathelicidin motif (ProS) of the protegrin-3 precursor was overexpressed in Escherichia coli as a His-tagged protein. The His(6) tag was removed by thrombin cleavage. ProS was purified to homogeneity and single crystals were obtained by the hanging-drop vapour-diffusion method at pH 3-4. Preliminary X-ray diffraction analysis indicated that these crystals belong to the hexagonal space group P6(1)22 or P6(5)22, with unit-cell parameters a = b = 51.42, c = 134.25 A. These crystals diffracted beyond 2.75 A (1.9 A at ESRF) and contain one molecule per asymmetric unit.

  3. single crystal growth, x-ray structure analysis, optical band gap ...

    African Journals Online (AJOL)

    2015-09-01

    Sep 1, 2015 ... absorption spectra illustrate the change in opticalband gap from 3.01eVto ... Keywords: Single crystal growth; structure analysis; optical Eg; Raman spectra; strain tensor ... Journal of Fundamental and Applied Sciences.

  4. Synthesis, characterization and single crystal X-ray analysis of chlorobis(N,N-dimethyldithiocarbamato-S,S′antimony(III

    Directory of Open Access Journals (Sweden)

    H.P.S. Chauhan

    2015-07-01

    Full Text Available The title compound chlorobis(N,N-dimethyldithiocarbamato-S,S′antimony(III has been prepared in distilled acetonitrile and characterized by physicochemical [melting point and molecular weight determination, elemental analysis (C, H, N, S & Sb], spectral [FT–IR, far IR, NMR (1H & 13C] studies. The crystal and molecular structure was further confirmed using single crystal X-ray diffraction analysis which features a five-coordinate geometry for antimony(III within a ClS4 donor set. The distortion in the co-planarity of ClSbS3 evidences the stereochemical influence exerts by the lone pair of electrons on antimony(III. Two centrosymmetrically related molecule held together via C–H···Cl secondary interaction result in molecular aggregation of the compound.

  5. Purification, crystallization and preliminary X-ray diffraction analysis of the kinase domain of human tousled-like kinase 2

    Energy Technology Data Exchange (ETDEWEB)

    Garrote, Ana M.; Redondo, Pilar [Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029 Madrid (Spain); Montoya, Guillermo, E-mail: gmontoya@cnio.es [Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029 Madrid (Spain); University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen (Denmark); Muñoz, Inés G., E-mail: gmontoya@cnio.es [Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029 Madrid (Spain)

    2014-02-19

    The C-terminal kinase domain of TLK2 (a human tousled-like kinase) has been cloned and overexpressed in Escherichia coli followed by purification to homogeneity. Crystallization experiments in the presence of ATP-γ-S yielded crystals suitable for X-ray diffraction analysis belonging to two different space groups: tetragonal I4{sub 1}22 and cubic P2{sub 1}3. Tousled-like kinases (TLKs) are an evolutionarily conserved family of serine/threonine protein kinases involved in chromatin dynamics, including DNA replication and repair, transcription and chromosome segregation. The two members of the family reported in humans, namely TLK1 and TLK2, localize to the cell nucleus and are capable of forming homo- or hetero-oligomers by themselves. To characterize the role of TLK2, its C-terminal kinase domain was cloned and overexpressed in Escherichia coli followed by purification to homogeneity. Crystallization experiments in the presence of ATP-γ-S yielded crystals suitable for X-ray diffraction analysis belonging to two different space groups: tetragonal I4{sub 1}22 and cubic P2{sub 1}3. The latter produced the best diffracting crystal (3.4 Å resolution using synchrotron radiation), with unit-cell parameters a = b = c = 126.05 Å, α = β = γ = 90°. The asymmetric unit contained one protein molecule, with a Matthews coefficient of 4.59 Å{sup 3} Da{sup −1} and a solvent content of 73.23%.

  6. Crystallization and preliminary X-ray crystallographic analysis of the sclerostin-neutralizing Fab AbD09097.

    Science.gov (United States)

    Boschert, Verena; Muth, Eva Maria; Knappik, Achim; Frisch, Christian; Mueller, Thomas D

    2015-04-01

    The secreted cystine-knot protein sclerostin was first identified from genetic screening of patients suffering from the rare bone-overgrowth diseases sclerosteosis and van Buchem disease. Sclerostin acts a negative regulator of bone growth through inhibiting the canonical Wnt signalling cascade by binding to and blocking the Wnt co-receptor LRP5/6. Its function in blocking osteoblastogenesis makes it an important target for osteoanabolic therapy approaches to treat osteoporosis, which is characterized by a progressive decrease in bone mass and density. In this work, the production, crystallization and preliminary X-ray diffraction data analysis of a sclerostin-neutralizing human Fab antibody fragment, AbD09097, obtained from a naive antibody library are reported. Crystals of the Fab AbD09097 belonged to space group P21, with unit-cell parameters a = 45.19, b = 78.49, c = 59.20 Å, β = 95.71° and diffracted X-rays to a resolution of 1.8 Å.

  7. Crystallization and preliminary X-ray analysis of ocr, the product of gene 0.3 of bacteriophage T7.

    Science.gov (United States)

    Sturrock, S S; Dryden, D T; Atanasiu, C; Dornan, J; Bruce, S; Cronshaw, A; Taylor, P; Walkinshaw, M D

    2001-11-01

    Ocr, the product of gene 0.3 of bacteriophage T7, prevents the action of restriction endonucleases of the host bacteria. The amino-acid sequence of ocr has less than 20% similarity to any protein of known three-dimensional structure. Ocr has been crystallized in a number of different crystal forms and X-ray data for the seleno-L-methionine-substituted form has been collected to a resolution of 1.8 A. The presence of caesium was found to be required for good crystal growth. Anomalous X-ray data was used to identify possible positions for Se and Cs atoms in the unit cell.

  8. Crystallization and Preliminary X-ray Diffraction Analysis of the Glucuronoyl Esterase Catalytic Domain from Hypocrea jecorina

    Science.gov (United States)

    The catalytic domain of the glucuronoyl esterase from Hypocrea jecorina (anamorph Trichoderma reesei) was over-expressed, purified, and crystallized by sitting-drop vapor-diffusion method using 1.4 M sodium/potassium phosphate pH 6.9. Crystals had space group P212121 and X-ray diffraction data were...

  9. Crystallization and preliminary X-ray analysis of Rv1674c from Mycobacterium tuberculosis

    Science.gov (United States)

    Li, Jincheng; Wang, Xudong; Gong, Weimin; Niu, Chunyan; Zhang, Min

    2015-01-01

    Adaptations to hypoxia play an important role in Mycobacterium tuberculosis pathogenesis. Rv0324, which contains an HTH DNA-binding domain and a rhodanese domain, is one of the key transcription regulators in response to hypoxia. M. tuberculosis Rv1674c is a homologue of Rv0324. To understand the interdomain interaction and regulation of the HTH domain and the rhodanese domain, recombinant Rv1674c protein was purified and crystallized by the vapour-diffusion method. The crystals diffracted to 2.25 Å resolution. Preliminary diffraction analysis suggests that the crystals belonged to space group P3121 or P3221, with unit-cell parameters a = b = 67.8, c = 174.5 Å, α = β = 90, γ = 120°. The Matthews coefficient was calculated to be 2.44 Å3 Da−1, assuming that the crystallographic asymmetric unit contains two protein molecules. PMID:25760714

  10. Crystallization and initial X-ray diffraction analysis of human pyruvate dehydrogenase

    Science.gov (United States)

    Ciszak, E.; Korotchkina, L. G.; Hong, Y. S.; Joachimiak, A.; Patel, M. S.

    2001-01-01

    Human pyruvate dehydrogenase (E1) is a component enzyme of the pyruvate dehydrogenase complex. The enzyme catalyzes the irreversible decarboxylation of pyruvic acid and the rate-limiting reductive acetylation of the lipoyl moiety linked to the dihydrolipoamide acetyltransferase component of the pyruvate dehydrogenase complex. E1 is an alpha(2)beta(2) tetramer ( approximately 154 kDa). Crystals of this recombinant enzyme have been grown in polyethylene glycol 3350 using a vapor-diffusion method at 295 K. The crystals are characterized as orthorhombic, space group P2(1)2(1)2(1), with unit-cell parameters a = 64.2, b = 126.9, c = 190.2 A. Crystals diffracted to a minimum d spacing of 2.5 A. The asymmetric unit contains one alpha(2)beta(2) tetrameric E1 assembly; self-rotation function analysis showed a pseudo-twofold symmetry relating the two alphabeta dimers.

  11. Crystallization and preliminary X-ray diffraction analysis of West Nile virus

    Energy Technology Data Exchange (ETDEWEB)

    Kaufmann, Barbel; Plevka, Pavel; Kuhn, Richard J.; Rossmann, Michael G. (Purdue)

    2010-05-25

    West Nile virus, a human pathogen, is closely related to other medically important flaviviruses of global impact such as dengue virus. The infectious virus was purified from cell culture using polyethylene glycol (PEG) precipitation and density-gradient centrifugation. Thin amorphously shaped crystals of the lipid-enveloped virus were grown in quartz capillaries equilibrated by vapor diffusion. Crystal diffraction extended at best to a resolution of about 25 {angstrom} using synchrotron radiation. A preliminary analysis of the diffraction images indicated that the crystals had unit-cell parameters a {approx_equal} b {approx_equal} 480 {angstrom}, {gamma} = 120{sup o}, suggesting a tight hexagonal packing of one virus particle per unit cell.

  12. Crystallization and preliminary X-ray analysis of the NKX2.5 homeodomain in complex with DNA.

    Science.gov (United States)

    Genis, Caroli; Scone, Peyton; Kasahara, Hideko; Nam, Hyun Joo

    2008-11-01

    As part of an effort to elucidate the molecular basis for the pathogenesis of NKX2.5 mutations in congenital heart disease using X-ray crystallography, the NKX2.5 homeodomain has been crystallized in complex with a specific DNA element, the -242 promoter region of atrial natriuretic factor. Crystals of the homeodomain-DNA complex diffracted X-rays to 1.7 A resolution and belonged to space group P6(5), with unit-cell parameters a = b = 71.5, c = 94.3 A. The asymmetric unit contained two molecules of the NKX2.5 homeodomain and one double-stranded oligonucleotide.

  13. Expression, purification, crystallization and preliminary X-ray diffraction analysis of the DDX3 RNA helicase domain.

    Science.gov (United States)

    Rodamilans, Bernardo; Montoya, Guillermo

    2007-04-01

    DDX3 is a human RNA helicase that is involved in RNA processing and important human diseases. This enzyme belongs to the DEAD-box protein family, the members of which are characterized by the presence of nine conserved motifs including the Asp-Glu-Ala-Asp motif that defines the family. DDX3 has two distinct domains: an ATP-binding domain in the central region of the protein and a helicase domain in the carboxy-terminal region. The helicase domain of DDX3 was cloned and overexpressed in Escherichia coli. Crystallization experiments yielded crystals that were suitable for X-ray diffraction analysis. The final crystallization conditions were a reservoir solution consisting of 2 M ammonium sulfate, 0.1 M imidazole pH 6.4 plus 5 mM spermine tetrahydrochloride and a protein solution containing 10 mM HEPES, 500 mM ammonium sulfate pH 8.0. The crystals of the helicase domain belong to the monoclinic space group P2(1), with unit-cell parameters a = 43.85, b = 60.72, c = 88.39 A, alpha = gamma = 90, beta = 101.02 degrees , and contained three molecules per asymmetric unit. These crystals diffracted to a resolution limit of 2.2 A using synchrotron radiation at the European Synchrotron Radiation Facility (ESRF) and the Swiss Light Source (SLS).

  14. Crystallization and preliminary X-ray crystallographic analysis of polyphenol oxidase from Juglans regia (jrPPO1)

    Energy Technology Data Exchange (ETDEWEB)

    Zekiri, Florime; Bijelic, Aleksandar; Molitor, Christian; Rompel, Annette, E-mail: annette.rompel@univie.ac.at [Universität Wien, Althanstrasse 14, 1090 Wien (Austria)

    2014-05-28

    The crystallization and preliminary X-ray crystallographic analysis of a plant PPO exhibiting monophenolase activity from J. regia (jrPPO1) in its active form (Asp{sup 101}–Arg{sup 445}) are reported. Tyrosinase is a type 3 copper enzyme that catalyzes the ortho-hydroxylation of monophenols to diphenols as well as their subsequent oxidation to quinones, which are precursors for the biosynthesis of melanins. The first plant tyrosinase from walnut leaves (Juglans regia) was purified to homogeneity and crystallized. During the purification, two forms of the enzyme differing only in their C-termini [jrPPO1(Asp{sup 101}–Pro{sup 444}) and jrPPO1(Asp{sup 101}–Arg{sup 445})] were obtained. The most abundant form jrPPO1(Asp{sup 101}–Arg{sup 445}), as described in Zekiri et al. [Phytochemistry (2014 ▶), 101, 5–15], was crystallized, resulting in crystals that belonged to space group C121, with unit-cell parameters a = 115.56, b = 91.90, c = 86.87 Å, α = 90, β = 130.186, γ = 90°, and diffracted to 2.39 Å resolution. Crystals were only obtained from solutions containing at least 30% polyethylene glycol 5000 monomethyl ether in a close-to-neutral pH range.

  15. Crystallization and preliminary X-ray diffraction analysis of a protease inhibitor from the haemolymph of the Indian tasar silkworm Antheraea mylitta

    Energy Technology Data Exchange (ETDEWEB)

    Roy, Sobhan [Department of Biotechnology, Indian Institute of Technology, Kharagpur (India); Aravind, Penmatsa [Centre for Cellular and Molecular Biology, Hyderabad (India); Madhurantakam, Chaithanya; Ghosh, Ananta Kumar [Department of Biotechnology, Indian Institute of Technology, Kharagpur (India); Sankaranarayanan, Rajan, E-mail: sankar@ccmb.res.in [Centre for Cellular and Molecular Biology, Hyderabad (India); Das, Amit Kumar, E-mail: sankar@ccmb.res.in [Department of Biotechnology, Indian Institute of Technology, Kharagpur (India)

    2006-07-01

    The crystallization and preliminary X-ray crystallographic analysis of a protease inhibitor from the haemolymph of the Indian tasar silk worm A. mylitta is reported. A protein with inhibitory activity against fungal proteases was purified from the haemolymph of the Indian tasar silkworm Antheraea mylitta and was crystallized using the hanging-drop vapour-diffusion method. Polyethylene glycol 3350 was used as a precipitant. Crystals belonged to space group P6{sub 3}22, with unit-cell parameters a = b = 60.6, c = 85.1 Å. X-ray diffraction data were collected and processed to a maximum resolution of 2.1 Å.

  16. Crystallization and preliminary X-ray analysis of Leishmania major glyoxalase I

    Energy Technology Data Exchange (ETDEWEB)

    Ariza, Antonio; Vickers, Tim J.; Greig, Neil; Fairlamb, Alan H.; Bond, Charles S., E-mail: c.s.bond@dundee.ac.uk [Division of Biological Chemistry and Molecular Microbiology, Wellcome Trust Biocentre, School of Life Sciences, University of Dundee, Dundee DD1 5EH,Scotland (United Kingdom)

    2005-08-01

    The detoxification enzyme glyoxalase I from L. major has been crystallized. Preliminary molecular-replacement calculations indicate the presence of three glyoxalase I dimers in the asymmetric unit. Glyoxalase I (GLO1) is a putative drug target for trypanosomatids, which are pathogenic protozoa that include the causative agents of leishmaniasis. Significant sequence and functional differences between Leishmania major and human GLO1 suggest that it may make a suitable template for rational inhibitor design. L. major GLO1 was crystallized in two forms: the first is extremely disordered and does not diffract, while the second, an orthorhombic form, produces diffraction to 2.0 Å. Molecular-replacement calculations indicate that there are three GLO1 dimers in the asymmetric unit, which take up a helical arrangement with their molecular dyads arranged approximately perpendicular to the c axis. Further analysis of these data are under way.

  17. Crystallization and preliminary X-ray diffraction analysis of Salmonella typhimurium uridine phosphorylase complexed with 5-fluorouracil.

    Science.gov (United States)

    Lashkov, A A; Gabdoulkhakov, A G; Shtil, A A; Mikhailov, A M

    2009-06-01

    Uridine phosphorylase (UPh; EC 2.4.2.3) catalyzes the phosphorolytic cleavage of the N-glycosidic bond of uridine to form ribose 1-phosphate and uracil. This enzyme also activates pyrimidine-containing drugs, including 5-fluorouracil (5-FU). In order to better understand the mechanism of the enzyme-drug interaction, the complex of Salmonella typhimurium UPh with 5-FU was cocrystallized using the hanging-drop vapour-diffusion method at 294 K. X-ray diffraction data were collected to 2.2 A resolution. Analysis of these data revealed that the crystal belonged to space group C2, with unit-cell parameters a = 158.26, b = 93.04, c = 149.87 A, alpha = gamma = 90, beta = 90.65 degrees . The solvent content was 45.85% assuming the presence of six hexameric molecules of the complex in the unit cell.

  18. Complex assembly, crystallization and preliminary X-ray crystallographic analysis of the human Rod–Zwilch–ZW10 (RZZ) complex

    Energy Technology Data Exchange (ETDEWEB)

    Altenfeld, Anika; Wohlgemuth, Sabine [Max Planck Institute of Molecular Physiology, Otto Hahn Strasse 11, 44227 Dortmund (Germany); Wehenkel, Annemarie [Institut Curie, CNRS UMR 3348/INSERM U1005, Bâtiment 110, Centre Universitaire, 91405 Orsay CEDEX (France); Vetter, Ingrid R. [Max Planck Institute of Molecular Physiology, Otto Hahn Strasse 11, 44227 Dortmund (Germany); Musacchio, Andrea, E-mail: andrea.musacchio@mpi-dortmund.mpg.de [Max Planck Institute of Molecular Physiology, Otto Hahn Strasse 11, 44227 Dortmund (Germany); University of Duisburg-Essen, Universitätstrasse 1, 45141 Essen (Germany)

    2015-03-20

    The 800 kDa complex of the human Rod, Zwilch and ZW10 proteins (the RZZ complex) was reconstituted in insect cells, purified, crystallized and subjected to preliminary X-ray diffraction analysis. The spindle-assembly checkpoint (SAC) monitors kinetochore–microtubule attachment during mitosis. In metazoans, the three-subunit Rod–Zwilch–ZW10 (RZZ) complex is a crucial SAC component that interacts with additional SAC-activating and SAC-silencing components, including the Mad1–Mad2 complex and cytoplasmic dynein. The RZZ complex contains two copies of each subunit and has a predicted molecular mass of ∼800 kDa. Given the low abundance of the RZZ complex in natural sources, its recombinant reconstitution was attempted by co-expression of its subunits in insect cells. The RZZ complex was purified to homogeneity and subjected to systematic crystallization attempts. Initial crystals containing the entire RZZ complex were obtained using the sitting-drop method and were subjected to optimization to improve the diffraction resolution limit. The crystals belonged to space group P3{sub 1} (No. 144) or P3{sub 2} (No. 145), with unit-cell parameters a = b = 215.45, c = 458.7 Å, α = β = 90.0, γ = 120.0°.

  19. Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Hubin, Elizabeth A.; Lilic, Mirjana; Darst, Seth A.; Campbell, Elizabeth A.

    2017-07-13

    The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the αCTD may play a role in Mtb transcription regulation. Our results reveal the structure of an Actinobacteria-unique insert of the RNAP β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σA, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.

  20. Crystallization and preliminary X-ray analysis of papaya mosaic virus coat protein.

    Science.gov (United States)

    Zhang, H; Todderud, E; Stubbs, G

    1993-12-05

    Papaya mosaic virus coat protein has been treated with trypsin and a large fragment of the intact protein has been crystallized in space group P3(1)21 or P3(2)21 (unit cell dimensions: a = b = 110 A, c = 237 A). The crystals diffract to 3.5 A resolution. Crystals of the untreated protein have also been grown. The untreated protein crystals diffract to 4 A resolution, but have a large mosaic spread. They have the same space group as the trypsin-treated protein crystals, but a much smaller unit cell (a = b = 72 A, c = 240 A).

  1. Crystallization and preliminary X-ray analysis of l-methionine γ-lyase 1 from Entamoeba histolytica

    Energy Technology Data Exchange (ETDEWEB)

    Sato, Dan [Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052 (Japan); Center for Integrated Medical Research, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582 (Japan); Department of Parasitology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511 (Japan); Karaki, Tsuyoshi; Shimizu, Akira; Kamei, Kaeko; Harada, Shigeharu, E-mail: harada@kit.ac.jp [Graduate School of Science and Technology, Department of Applied Biology, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585 (Japan); Nozaki, Tomoyoshi [Department of Parasitology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511 (Japan); Department of Parasitology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640 (Japan); Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052 (Japan)

    2008-08-01

    l-Methionine γ-lyase 1, a key enzyme in sulfur-containing amino-acid degradation, from the protozoan parasite E. histolytica was crystallized in a form suitable for X-ray structure analysis. l-Methionine γ-lyase (MGL) is a pyridoxal phosphate-dependent enzyme that is involved in the degradation of sulfur-containing amino acids. MGL is an attractive drug target against amoebiasis because the mammalian host of its causative agent Entamoeba histolytica lacks MGL. For the development of anti-amoebic agents based on the structure of MGL, one of two MGL isoenzymes (EhMGL1) was crystallized in the monoclinic space group P2{sub 1}, with unit-cell parameters a = 99.12, b = 85.38, c = 115.37 Å, β = 101.82°. The crystals diffract to beyond 2.0 Å resolution. The presence of a tetramer in the asymmetric unit (4 × 42.4 kDa) gives a Matthews coefficient of 2.8 Å{sup 3} Da{sup −1} and a solvent content of 56%. The structure was solved by the molecular-replacement method and structure refinement is now in progress.

  2. The SecB-like chaperone Rv1957 from Mycobacterium tuberculosis: crystallization and X-ray crystallographic analysis.

    Science.gov (United States)

    Lu, Zuokun; Wang, Han; Yu, TingTing

    2016-06-01

    Protein export is important in all bacteria, and bacteria have evolved specialized export machineries to fulfil this task. In Mycobacterium tuberculosis, the causative agent of tuberculosis, the general secretion pathway (Sec pathway) is conserved and is essential in performing the export of proteins. The bacterial Sec pathway post-translationally exports unfolded proteins out of the cytoplasm, and the core of the Sec pathway is composed of a heterotrimeric membrane-embedded channel, SecYEG, and two cytosolic components, SecA and SecB. SecB functions by stabilizing unfolded proteins, maintaining them in an export-competent state. Although SecB is mainly found in Proteobacteria, a SecB-like protein, Rv1957, that controls a stress-response toxin-antitoxin system, is found in M. tuberculosis. Rv1957 can also functionally replace the Escherichia coli SecB chaperone both in vivo and in vitro. In this work, the production, crystallization and X-ray crystallographic analysis of Rv1957 are reported. Notably, diffraction-quality crystals were obtained only at high concentrations of dimethyl sulfoxide, i.e. about 12%(v/v). The crystals of Rv1957 belonged to space group P212121, with unit-cell parameters a = 64.5, b = 92.0, c = 115.4 Å.

  3. Photonic crystals at visible, x-ray, and terahertz frequencies

    Science.gov (United States)

    Prasad, Tushar

    Photonic crystals are artificial structures with a periodically varying refractive index. This property allows photonic crystals to control the propagation of photons, making them desirable components for novel photonic devices. Photonic crystals are also termed as "semiconductors of light", since they control the flow of electromagnetic radiation similar to the way electrons are excited in a semiconductor crystal. The scale of periodicity in the refractive index determines the frequency (or wavelength) of the electromagnetic waves that can be manipulated. This thesis presents a detailed analysis of photonic crystals at visible, x-ray, and terahertz frequencies. Self-assembly and spin-coating methods are used to fabricate colloidal photonic crystals at visible frequencies. Their dispersion characteristics are examined through theoretical as well as experimental studies. Based on their peculiar dispersion property called the superprism effect, a sensor that can detect small quantities of chemical substances is designed. A photonic crystal that can manipulate x-rays is fabricated by using crystals of a non-toxic plant virus as templates. Calculations show that these metallized three-dimensional crystals can find utility in x-ray optical systems. Terahertz photonic crystal slabs are fabricated by standard lithographic and etching techniques. In-plane superprism effect and out-of-plane guided resonances are studied by terahertz time-domain spectroscopy, and verified by numerical simulations.

  4. Crystallization and preliminary X-ray analysis of a phosphopentomutase from Bacillus cereus

    Energy Technology Data Exchange (ETDEWEB)

    Panosian, Timothy D.; Nannemann, David P.; Bachmann, Brian O.; Iverson, T.M. (Vanderbilt)

    2013-09-18

    Phosphopentomutases (PPMs) interconvert D-ribose 5-phosphate and {alpha}-D-ribose 1-phosphate to link glucose and nucleotide metabolism. PPM from Bacillus cereus was overexpressed in Escherichia coli, purified to homogeneity and crystallized. Bacterial PPMs are predicted to contain a di-metal reaction center, but the catalytically relevant metal has not previously been identified. Sparse-matrix crystallization screening was performed in the presence or absence of 50 mM MnCl{sub 2}. This strategy resulted in the formation of two crystal forms from two chemically distinct conditions. The crystals that formed with 50 mM MnCl{sub 2} were more easily manipulated and diffracted to higher resolution. These results suggest that even if the catalytically relevant metal is not known, the crystallization of putative metalloproteins may still benefit from supplementation of the crystallization screens with potential catalytic metals.

  5. Purification, crystallization and preliminary X-ray analysis of CMS1MS2: a cysteine proteinase from Carica candamarcensis latex

    Science.gov (United States)

    Gomes, Marco Túlio Ribeiro; Teixeira, Raphael Dias; Ribeiro, Henrique de Assis Lopes; Turchetti, Andréia Pereira; Junqueira, Caroline Furtado; Lopes, Míriam Tereza Paz; Salas, Carlos Edmundo; Nagem, Ronaldo Alves Pinto

    2008-01-01

    Cysteine proteinases from the latex of plants of the family Caricaceae are widely used industrially as well as in pharmaceutical preparations. In the present work, a 23 kDa cysteine proteinase from Carica candamarcensis latex (designated CMS1MS2) was purified for crystallization using three chromatography steps. The enzyme shows about fourfold higher activity than papain with BAPNA as substrate. Crystals suitable for X-ray diffraction experiments were obtained by the hanging-drop method in the presence of PEG and ammonium sulfate as precipitants. The crystals are monoclinic (space group P21), with unit-cell parameters a = 53.26, b = 75.71, c = 53.23 Å, β = 96.81°, and diffract X-rays to 1.8 Å resolution. PMID:18540057

  6. Purification, crystallization and preliminary X-ray analysis of an acetylxylan esterase from Bacillus pumilus.

    Science.gov (United States)

    Benini, S; Degrassi, G; Krastanova, I; Lamba, D; Venturi, V

    2001-12-01

    The gene encoding for acetylxylan esterase from Bacillus pumilus has been cloned and expressed in Escherichia coli. The recombinant protein has been purified to homogeneity and crystallized. The crystals obtained are of regular shape of dimensions 0.05 x 0.05 x 0.05 mm with R32 symmetry and diffract to 2.0 A using synchrotron radiation.

  7. Crystallization and preliminary X-ray analysis of Streptococcus mutans dextran glucosidase

    Energy Technology Data Exchange (ETDEWEB)

    Saburi, Wataru; Hondoh, Hironori, E-mail: hondoh@abs.agr.hokudai.ac.jp [Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589 (Japan); Unno, Hideaki [Faculty of Engineering, Nagasaki University, Bunkyo-machi, Nagasaki 852-8521 (Japan); Okuyama, Masayuki; Mori, Haruhide [Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589 (Japan); Nakada, Toshitaka [Faculty of Science and Engineering, Ritsumeikan University, Kusatsu, Shiga 525-8577 (Japan); Matsuura, Yoshiki [Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 (Japan); Kimura, Atsuo [Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589 (Japan)

    2007-09-01

    Dextran glucosidase from S. mutans was crystallized using the hanging-drop vapour-diffusion method. The crystals diffracted to 2.2 Å resolution. Dextran glucosidase from Streptococcus mutans is an exo-hydrolase that acts on the nonreducing terminal α-1,6-glucosidic linkage of oligosaccharides and dextran with a high degree of transglucosylation. Based on amino-acid sequence similarity, this enzyme is classified into glycoside hydrolase family 13. Recombinant dextran glucosidase was purified and crystallized by the hanging-drop vapour-diffusion technique using polyethylene glycol 6000 as a precipitant. The crystals belong to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 72.72, b = 86.47, c = 104.30 Å. A native data set was collected to 2.2 Å resolution from a single crystal.

  8. Crystallization and preliminary X-ray analysis of pectin lyase A from Aspergillus niger.

    Science.gov (United States)

    Jenkins, J; Scott, M; Mayans, O; Pickersgill, R; Harris, G; Connerton, I; Gravesen, T

    1996-03-01

    The major secreted pectin lyase (E.C. 4.2.2.10) from Aspergillus niger, strain 4M-147, has been purified and crystallized by the hanging-drop method using polyethylene glycol as precipitant. The crystals belong to the space group P2(1)2(1)2(1) with cell dimensions a = 45.2, b = 83.2, c = 93.1 A (1 A = 0.1 nm) and a single molecule in the asymmetric unit. The crystals diffract to at least 2.0 A resolution and are suitable for structure determination.

  9. Crystallization and preliminary X-ray crystallographic analysis of human geranylgeranyl pyrophosphate synthase

    Institute of Scientific and Technical Information of China (English)

    CHEN Yushu; LI Xiaofeng; LOU Zhiyong; WANG Weina; PANG Hai; RAO Zihe

    2006-01-01

    Human geranylgeranyl pyrophosphate synthase (GGPS) is an enzyme that catalyzes the synthesis of geranylgeranyl py rophosphate (GGPP) from farnesyldiphosphate and isopentenyldiphosphate. Recombinant human GGPS was crystallized by the hanging-drop vapor diffusion method. Crystals were grown at 18℃ using PEG 4000 as precipitant. Diffraction data were obtained to a resolution of 2.8 (A) from a single frozen crystal belonging to space group PI, with unit-cell parameters: α = 68.9 (A), b = 107.7 (A), c = 137.4 (A),α=99.6°, β=97.6°, γ=97.8°.

  10. Crystallization and preliminary X-ray diffraction analysis of the hyperthermophilic Sulfolobus solfataricus phosphotriesterase

    Energy Technology Data Exchange (ETDEWEB)

    Elias, Mikael [Laboratoire de Cristallographie et Modélisation des Matériaux Minéraux et Biologiques, CNRS-Université Henri Poincaré, 54506 Vandoeuvre-lès-Nancy (France); Dupuy, Jérôme [Laboratoire de Cristallogenèse et Cristallographie des Protéines, Institut de Biologie Structurale J.-P. Ebel, 38027 Grenoble (France); Merone, Luigia [Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Napoli (Italy); Lecomte, Claude [Laboratoire de Cristallographie et Modélisation des Matériaux Minéraux et Biologiques, CNRS-Université Henri Poincaré, 54506 Vandoeuvre-lès-Nancy (France); Rossi, Mosè [Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Napoli (Italy); Masson, Patrick [Unité d’Enzymologie, Département de Toxicologie, Centre de Recherches du Service de Santé des Armées, 38702 La Tronche (France); Manco, Giuseppe [Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Napoli (Italy); Chabriere, Eric, E-mail: eric.chabriere@lcm3b.uhp-nancy.fr [Laboratoire de Cristallographie et Modélisation des Matériaux Minéraux et Biologiques, CNRS-Université Henri Poincaré, 54506 Vandoeuvre-lès-Nancy (France); Unité d’Enzymologie, Département de Toxicologie, Centre de Recherches du Service de Santé des Armées, 38702 La Tronche (France)

    2007-07-01

    A phosphotriesterase (PTE) from the hyperthermophilic archaeon S. solfataricus has been crystallized. Combined with biochemical and bioengineering studies, it is expected that the structure of this protein will provide insight into the natural function of the PTE family and provide important data for achieving an efficient organophosphate biodecontaminant. Organophosphates constitute the largest class of insecticides used worldwide and some of them are potent nerve agents. Consequently, organophosphate-degrading enzymes are of paramount interest as they could be used as bioscavengers and biodecontaminants. Phosphotriesterases (PTEs) are capable of hydrolyzing these toxic compounds with high efficiency. A distant and hyperthermophilic representative of the PTE family was cloned from the archeon Sulfolobus solfataricus MT4, overexpressed in Escherichia coli and crystallized; the crystals diffracted to 2.54 Å resolution. Owing to its exceptional thermostability, this PTE may be an excellent candidate for obtaining an efficient organophosphate biodecontaminant. Here, the crystallization conditions and data collection for the hyperthermophilic S. solfataricus PTE are reported.

  11. LCP crystallization and X-ray diffraction analysis of VcmN, a MATE transporter from Vibrio cholerae

    Energy Technology Data Exchange (ETDEWEB)

    Kusakizako, Tsukasa [Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan); Tanaka, Yoshiki [Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192 (Japan); Hipolito, Christopher J. [Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575 (Japan); Kuroda, Teruo [Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553 (Japan); Ishitani, Ryuichiro [Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan); Suga, Hiroaki [Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Nureki, Osamu, E-mail: nureki@bs.s.u-tokyo.ac.jp [Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan)

    2016-06-22

    A V. cholerae MATE transporter was crystallized using the lipidic cubic phase (LCP) method. X-ray diffraction data sets were collected from single crystals obtained in a sandwich plate and a sitting-drop plate to resolutions of 2.5 and 2.2 Å, respectively. Multidrug and toxic compound extrusion (MATE) transporters, one of the multidrug exporter families, efflux xenobiotics towards the extracellular side of the membrane. Since MATE transporters expressed in bacterial pathogens contribute to multidrug resistance, they are important therapeutic targets. Here, a MATE-transporter homologue from Vibrio cholerae, VcmN, was overexpressed in Escherichia coli, purified and crystallized in lipidic cubic phase (LCP). X-ray diffraction data were collected to 2.5 Å resolution from a single crystal obtained in a sandwich plate. The crystal belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 52.3, b = 93.7, c = 100.2 Å. As a result of further LCP crystallization trials, crystals of larger size were obtained using sitting-drop plates. X-ray diffraction data were collected to 2.2 Å resolution from a single crystal obtained in a sitting-drop plate. The crystal belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 61.9, b = 91.8, c = 100.9 Å. The present work provides valuable insights into the atomic resolution structure determination of membrane transporters.

  12. Purification, crystallization and preliminary X-ray diffraction analysis of a plant subtilase.

    Science.gov (United States)

    Rose, Rolf; Huttenlocher, Franziska; Cedzich, Anna; Kaiser, Markus; Schaller, Andreas; Ottmann, Christian

    2009-05-01

    The subtilase SBT3 from Solanum lycopersicum (tomato) was purified from a tomato cell culture and crystallized using the sitting-drop vapour-diffusion method. A native data set was collected to 2.5 A resolution at 100 K using synchrotron radiation. For experimental phasing, CsCl-derivative and tetrakis(acetoxymercuri)methane (TAMM) derivative crystals were employed for MIRAS phasing. Three caesium sites and one TAMM site were identified, which allowed solution of the structure.

  13. Crystallization and preliminary X-ray diffraction analysis of the magnesium transporter CorA.

    Science.gov (United States)

    Payandeh, Jian; Pai, Emil F

    2006-02-01

    The full-length integral membrane protein CorA from Thermotoga maritima (TmCorA(1-351)) has been expressed in Escherichia coli and purified without membrane isolation. TmCorA(1-351) crystallized in the monoclinic space group C2, with unit-cell parameters a = 214.25, b = 86.30, c = 181.53 A, beta = 112.23 degrees. Native crystals diffracted to 3.7 A using synchrotron radiation, but selenomethionine-substituted crystals rarely diffracted to better than 5.0 A. All full-length protein crystals were highly mosaic and produced anisotropic diffraction patterns. To aid in crystallographic phasing, soluble domain constructs were screened and the periplasmic domain of CorA from Archaeoglobus fulgidus (AfCorA(1-263)) was crystallized in the hexagonal space group P6(1)22, with unit-cell parameters a = b = 101.17, c = 142.87 A. Native and SeMet-substituted AfCorA(1-263) crystals diffracted to approximately 3.0 A using synchrotron radiation.

  14. Expression, purification, crystallization and preliminary X-ray analysis of Pseudomonas aeruginosa AlgX

    Energy Technology Data Exchange (ETDEWEB)

    Weadge, J.T.; Robinson, H.; Yip, P. P.; Arnett, K.; Tipton, P. A.; Howell, P. L.

    2010-05-01

    AlgX is a periplasmic protein required for the production of the exopolysaccharide alginate in Pseudomonas sp. and Azotobacter vinelandii. AlgX has been overexpressed and purified and diffraction-quality crystals have been grown using iterative seeding and the hanging-drop vapor-diffusion method. The crystals grew as flat plates with unit-cell parameters a = 46.4, b = 120.6, c = 86.9 {angstrom}, {beta} = 95.7{sup o}. The crystals exhibited the symmetry of space group P2{sub 1} and diffracted to a minimum d-spacing of 2.1 {angstrom}. On the basis of the Matthews coefficient (V{sub M} = 2.25 {angstrom}{sup 3} Da{sup -1}), two molecules were estimated to be present in the asymmetric unit.

  15. Crystallization and preliminary X-ray diffraction analysis of the fructofuranosidase from Xanthophyllomyces dendrorhous.

    Science.gov (United States)

    Polo, Aitana; Linde, Dolores; Estévez, Marta; Fernández-Lobato, María; Sanz-Aparicio, Julia

    2010-11-01

    Xanthophyllomyces dendrorhous invertase is an extracellular enzyme that releases β-fructose from the nonreducing termini of various β-D-fructofuranoside substrates. Its ability to produce neokestose by transglycosylation makes this enzyme an interesting research target for applications in industrial biotechnology. The native enzyme, which is highly glycosylated, failed to crystallize. Therefore, it was submitted to EndoH deglycosylating treatment and crystals were grown by vapour-diffusion methods. The crystals belonged to space group P2(1)2(1)2, with unit-cell parameters a = 75.29, b = 204.93, c = 146.25 Å. Several diffraction data sets were collected using a synchrotron source. Self-rotation function and gel-filtration experiments suggested that the enzyme is a dimer with twofold symmetry.

  16. Expression, purification, crystallization and preliminary X-ray analysis of Aeromonas hydrophilia metallo-[beta]-lactamase

    Energy Technology Data Exchange (ETDEWEB)

    Sharma, N.; Toney, J.H.; Fitzgerald, P.M.D. (Merck)

    2010-07-20

    The CphA metallo-{beta}-lactamase from Aeromonas hydrophilia has been expressed, purified and crystallized by the hanging-drop vapor-diffusion method using ammonium sulfate as the precipitant. The crystals exhibit orthorhombic symmetry (P2{sub 1}2{sub 1}2), with unit-cell parameters a = 40.75, b = 42.05, c = 128.88 {angstrom}. There is one monomer in the asymmetric unit and the solvent content is estimated to be 44% by volume. A data set extending to 1.8 {angstrom} has been measured.

  17. Crystallization and initial X-ray diffraction analysis of a mannose-binding lectin from champedak.

    Science.gov (United States)

    Gabrielsen, Mads; Abdul-Rahman, Puteri Shafinaz; Isaacs, Neil W; Hashim, Onn Haji; Cogdell, Richard J

    2010-05-01

    Mannose-binding lectin from champedak (Artocarpus integer) is a homotetramer with a single-monomer molecular weight of 16 800 Da. Previous work has shown it to bind IgE and IgM, as well as being a mitogen of T cells in humans. Champedak mannose-binding lectin has successfully been used to detect altered glycosylation states of serum proteins. The protein was crystallized at 293 K in space group P2(1)2(1)2(1) (unit-cell parameters a = 76.89, b = 86.22, c = 95.37 A) and the crystals diffracted to 2.0 A resolution.

  18. Expression purification crystallization and preliminary X-ray analysis of Pseudomonas aeruginosa PelD

    Energy Technology Data Exchange (ETDEWEB)

    Marmont L. S.; Robinson H.; Whitney J. C.; Colvin K. M.; Parsek M. R.; Howell P. L.

    2012-02-01

    The production of the PEL polysaccharide in Pseudomonas aeruginosa requires the binding of bis-(3',5')-cyclic dimeric guanosine monophosphate (c-di-GMP) to the cytoplasmic GGDEF domain of the inner membrane protein PelD. Here, the overexpression, purification and crystallization of a soluble construct of PelD that encompasses the GGDEF domain and a predicted GAF domain is reported. Diffraction-quality crystals were grown using the hanging-drop vapour-diffusion method. The crystals grew as flat plates, with unit-cell parameters a = 88.3, b = 114.0, c = 61.9 {angstrom}, {alpha} = {beta} = {gamma} = 90.0{sup o}. The PelD crystals exhibited the symmetry of space group P2{sub 1}2{sub 1}2 and diffracted to a minimum d-spacing of 2.2 {angstrom}. On the basis of the Matthews coefficient (V{sub M} = 2.29 {angstrom}{sup 3} Da{sup -1}), it was estimated that two molecules are present in the asymmetric unit.

  19. Crystallization and X-ray analysis of the salmon-egg lectin SEL24K

    OpenAIRE

    Murata, Kenji; Andrew J. Fisher; Hedrick, Jerry L

    2007-01-01

    The 24 kDa egg lectin of Chinook salmon (Oncorhynchus tshawytscha) was purified by affinity chromatography from salmon eggs and crystallized by the hanging-drop vapor-diffusion method using 15/4 EO/OH (pentaerythritol ethoxylate) as a precipitant.

  20. Full analysis of feldspar texture and crystal structure by combining X-ray and electron techniques

    DEFF Research Database (Denmark)

    Balic Zunic, Tonci; Piazolo, Sandra; Katerinopoulou, Anna;

    2013-01-01

    identification plus crystal structure refinement of all components in a feldspar intergrowth. This procedure was applied to perthitic intergrowths in feldspars from two different pegmatites in the Larvik plutonic complex in the southern part of the Oslo region, Norway. It revealed that the two starting high...

  1. Purification, crystallization and preliminary X-ray diffraction analysis of an archaeal ABC-ATPase

    NARCIS (Netherlands)

    Verdon, Grégory; Albers, Sonja-V.; Dijkstra, Bauke W.; Driessen, Arnold J.M.; Thunnissen, Andy-Mark W.H.

    2002-01-01

    In the archaeon Sulfolobus solfataricus glucose uptake is mediated by an ABC transport system. The ABC-ATPase of this transporter (GlcV) has been overproduced in Escherichia coli and purified. Crystals of GlcV suitable for data collection were obtained in the absence of nucleotide by microseeding

  2. Spatiotemporal Response of Crystals in X-ray Bragg Diffraction

    CERN Document Server

    Shvyd'ko, Yuri

    2012-01-01

    The spatiotemporal response of crystals in x-ray Bragg diffraction resulting from excitation by an ultra-short, laterally confined x-ray pulse is studied theoretically. The theory presents an extension of the analysis in symmetric reflection geometry [1] to the generic case, which includes Bragg diffraction both in reflection (Bragg) and transmission (Laue) asymmetric scattering geometries. The spatiotemporal response is presented as a product of a crystal-intrinsic plane wave spatiotemporal response function and an envelope function defined by the crystal-independent transverse profile of the incident beam and the scattering geometry. The diffracted wavefields exhibit amplitude modulation perpendicular to the propagation direction due to both angular dispersion and the dispersion due to Bragg's law. The characteristic measure of the spatiotemporal response is expressed in terms of a few parameters: the extinction length, crystal thickness, Bragg angle, asymmetry angle, and the speed of light. Applications to...

  3. Expression, crystallization and preliminary X-ray crystallographic analysis of alcohol dehydrogenase (ADH) from Kangiella koreensis.

    Science.gov (United States)

    Ngo, Ho-Phuong-Thuy; Hong, Seung-Hye; Hong, Myoung-Ki; Pham, Tan-Viet; Oh, Deok-Kun; Kang, Lin-Woo

    2013-09-01

    Alcohol dehydrogenases (ADHs) are a group of dehydrogenase enzymes that facilitate the interconversion between alcohols and aldehydes or ketones with the reduction of NAD(+) to NADH. In bacteria, some alcohol dehydrogenases catalyze the opposite reaction as part of fermentation to ensure a constant supply of NAD(+). The adh gene from Kangiella koreensis was cloned and the protein (KkADH) was expressed, purified and crystallized. A KkADH crystal diffracted to 2.5 Å resolution and belonged to the monoclinic space group P2(1), with unit-cell parameters a = 94.1, b = 80.9, c = 115.6 Å, β = 111.9°. Four monomers were present in the asymmetric unit, with a corresponding VM of 2.55 Å(3) Da(-1) and a solvent content of 51.8%.

  4. Overexpression, crystallization and preliminary X-ray crystallographic analysis of the ectoine hydroxylase from Sphingopyxis alaskensis.

    Science.gov (United States)

    Hoeppner, Astrid; Widderich, Nils; Bremer, Erhard; Smits, Sander H J

    2014-04-01

    The ectoine hydroxylase (EctD) is a member of the non-haem-containing iron(II)- and 2-oxoglutarate-dependent dioxygenase superfamily. Its mononuclear iron centre is a prerequisite for the activity of this enzyme and promotes the O2-dependent oxidative decarboxylation of 2-oxoglutarate, which is coupled to a two-electron oxidation of the substrate ectoine to yield 5-hydroxyectoine. An expression and purification protocol for the EctD enzyme from Sphingopyxis alaskensis was developed and the protein was crystallized using the sitting-drop vapour-diffusion method. This resulted in two different crystal forms, representing the apo and iron-bound forms of the enzyme.

  5. Crystallization and preliminary X-ray diffraction analysis of rat protein tyrosine phosphatase η

    Energy Technology Data Exchange (ETDEWEB)

    Matozo, Huita C.; Nascimento, Alessandro S.; Santos, Maria A. M. [Instituto de Física de São Carlos, Departamento de Física e Informática, Universidade de São Paulo, Avenida Trabalhador São Carlense 400, CEP 13566-590 São Carlos, SP (Brazil); Iuliano, Rodolfo [Dipartimento di Medicina Sperimentale e Clinica, Facoltà di Medicina e Chirurgia, Università di Catanzaro, 88100 Catanzaro (Italy); Fusco, Alfredo [Dipartimento di Biologia e Patologia Cellulare e Molecolare, c/o Instituto di Endocrinologia ed Oncologia Sperimentale del CNR, Facolta di Medicina e Chirurgia, Università degli Studi di Napoli ‘Federico II’, Via Pansini 5, 80131 Naples (Italy); NOGEC (Naples Oncogenomocs Center)-CEINGE, Biotecnologie Avanzate, Via Comunale Margherita 482, 80145 Naples (Italy); Polikarpov, Igor, E-mail: ipolikarpov@if.sc.usp.br [Instituto de Física de São Carlos, Departamento de Física e Informática, Universidade de São Paulo, Avenida Trabalhador São Carlense 400, CEP 13566-590 São Carlos, SP (Brazil); Laboratório Nacional de Luz Síncrotron, Campinas, SP (Brazil)

    2006-09-01

    In this study, the catalytic domain of rat protein tyrosine phosphatase η was produced in Escherichia coli in soluble form and purified to homogeneity. Crystals were obtained by the hanging-drop vapour-diffusion method. The rat protein tyrosine phosphatase η (rPTPη) is a cysteine-dependent phosphatase which hydrolyzes phosphoester bonds in proteins and other molecules. rPTPη and its human homologue DEP-1 are involved in neoplastic transformations. Thus, expression of the protein is reduced in all oncogene-transformed thyroid cell lines and is absent in highly malignant thyroid cells. Moreover, consistent with the suggested tumour suppression role of PTPη, inhibition of the tumorigenic process occurs after its exogenous reconstitution, suggesting that PTPη might be important for gene therapy of cancers. In this study, the catalytic domain of rPTPη was produced in Escherichia coli in soluble form and purified to homogeneity. Crystals were obtained by the hanging-drop vapour-diffusion method. Diffraction data were collected to 1.87 Å resolution. The crystal belongs to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 46.46, b = 63.07, c = 111.64 Å, and contains one molecule per asymmetric unit.

  6. Crystallization and preliminary X-ray analysis of Ebola VP35 interferon inhibitory domain mutant proteins

    Energy Technology Data Exchange (ETDEWEB)

    Leung, Daisy W.; Borek, Dominika; Farahbakhsh, Mina; Ramanan, Parameshwaran; Nix, Jay C.; Wang, Tianjiao; Prins, Kathleen C.; Otwinowski, Zbyszek; Honzatko, Richard B.; Helgeson, Luke A.; Basler, Christopher F.; Amarasinghe, Gaya K. (Texas-HSC); (Sinai); (Iowa State); (LBNL)

    2010-06-21

    VP35 is one of seven structural proteins encoded by the Ebola viral genome and mediates viral replication, nucleocapsid formation and host immune suppression. The C-terminal interferon inhibitory domain (IID) of VP35 is critical for dsRNA binding and interferon inhibition. The wild-type VP35 IID structure revealed several conserved residues that are important for dsRNA binding and interferon antagonism. Here, the expression, purification and crystallization of recombinant Zaire Ebola VP35 IID mutants R312A, K319A/R322A and K339A in space groups P6{sub 1}22, P2{sub 1}2{sub 1}2{sub 1} and P2{sub 1}, respectively, are described. Diffraction data were collected using synchrotron sources at the Advanced Light Source and the Advanced Photon Source.

  7. Crystallization and X-ray structure analysis of a thermostable penicillin G acylase from Alcaligenes faecalis

    Science.gov (United States)

    Varshney, Nishant Kumar; Suresh Kumar, R.; Ignatova, Zoya; Prabhune, Asmita; Pundle, Archana; Dodson, Eleanor; Suresh, C. G.

    2012-01-01

    The enzyme penicillin G acylase (EC 3.5.1.11) catalyzes amide-bond cleavage in benzylpenicillin (penicillin G) to yield 6-aminopenicillanic acid, an intermediate chemical used in the production of semisynthetic penicillins. A thermostable penicillin G acylase from Alcaligenes faecalis (AfPGA) has been crystallized using the hanging-drop vapour-diffusion method in two different space groups: C2221, with unit-cell parameters a = 72.9, b = 86.0, c = 260.2 Å, and P41212, with unit-cell parameters a = b = 85.6, c = 298.8 Å. Data were collected at 293 K and the structure was determined using the molecular-replacement method. Like other penicillin acylases, AfPGA belongs to the N-terminal nucleophilic hydrolase superfamily, has undergone post-translational processing and has a serine as the N-­terminal residue of the β-chain. A disulfide bridge has been identified in the structure that was not found in the other two known penicillin G acylase structures. The presence of the disulfide bridge is perceived to be one factor that confers higher stability to this enzyme. PMID:22442220

  8. Crystallization and preliminary X-ray crystallographic analysis of a highly specific serpin from the beetle Tenebrio molitor.

    Science.gov (United States)

    Park, Sun Hee; Piao, Shunfu; Kwon, Hyun Mi; Kim, Eun Hye; Lee, Bok Luel; Ha, Nam Chul

    2010-02-01

    The Toll signalling pathway, which is crucial for innate immunity, is transduced in insect haemolymph via a proteolytic cascade consisting of three serine proteases. The proteolytic cascade is downregulated by a specific serine protease inhibitor (serpin). Recently, the serpin SPN48 was found to show an unusual specific reactivity towards the terminal serine protease, Spätzle-processing enzyme, in the beetle Tenebrio molitor. In this study, the mature form of SPN48 was overexpressed in Escherichia coli and purified. The purified SPN48 protein was crystallized using 14% polyethylene glycol 8000 and 0.1 M 2-(N-morpholino)ethanesulfonic acid pH 6.0 as the precipitant. The crystals diffracted X-rays to 2.1 A resolution and were suitable for structure determination. The crystals belonged to space group P2(1). The crystal structure will provide information regarding how SPN48 achieves its unusual specificity for its target protease.

  9. Cloning, expression, purification, crystallization and X-ray crystallographic analysis of ScpB (Rv1710) from Mycobacterium tuberculosis

    Energy Technology Data Exchange (ETDEWEB)

    Kwon, Soo-Young [Beamline Division, Pohang Accelerator Laboratory, Pohang, Kyungbuk 790-784 (Korea, Republic of); Kang, Beom Sik [School of Life Science and Biotechnology, Kyungpook National University, Daegu 702-701 (Korea, Republic of); Kim, Myung Hee [Systems Microbiology Research Center, Korea Research Institute of Biosciences and Biotechnology, Yusung, Daejon 305-806 (Korea, Republic of); Kim, Kyung Jin, E-mail: kkj@postech.ac.kr [Beamline Division, Pohang Accelerator Laboratory, Pohang, Kyungbuk 790-784 (Korea, Republic of)

    2007-12-01

    ScpB from M. tuberculosis was crystallized using the sitting-drop vapour-diffusion method in the presence of 2 M NaCl and 10% PEG 6000 at 295 K. X-ray diffraction data were collected to a maximum resolution of 2.3 Å at a synchrotron beamline. Structural maintenance of chromosome (SMC) proteins play diverse roles in cellular DNA reassembly by directly interacting with DNA. They require non-SMC proteins for their proper function; these include the conserved segregation and condensation proteins (Scps) in prokaryotes. ScpB from Mycobacterium tuberculosis was crystallized using the sitting-drop vapour-diffusion method in the presence of 2 M NaCl and 10% PEG 6000 at 295 K. X-ray diffraction data were collected to a maximum resolution of 2.3 Å at a synchrotron beamline. The crystal belongs to the hexagonal space group R32, with unit-cell parameters a = b = 136.69, c = 78.55 Å, γ = 120°. With one molecule per asymmetric unit, the crystal volume per unit protein weight (V{sub M}) is 2.95 Å{sup 3} Da{sup −1}. The structure was solved by the single anomalous dispersion method and structure refinement is in progress.

  10. Crystallization and preliminary X-ray diffraction analysis of the haem-binding protein HemS from Yersinia enterocolitica

    Energy Technology Data Exchange (ETDEWEB)

    Schneider, Sabine; Paoli, Massimo, E-mail: max.paoli@nottingham.ac.uk [School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD (United Kingdom)

    2005-08-01

    The haem binding protein HemS from Y. enterocolitica has been crystallized in complex with its ligand. The crystals diffracted X-rays to 2.6 Å in-house. Bacteria have evolved strategies to acquire iron from their environment. Pathogenic microbes rely on specialized proteins to ‘steal’ haem from their host and use it as an iron source. HemS is the ultimate recipient of a molecular-relay system for haem uptake in Gram-negative species, functioning as the cytosolic carrier of haem. Soluble expression and high-quality diffraction crystals were obtained for HemS from Yersinia enterocolitica. Crystals belong to the orthorhombic space group I222, with unit-cell parameters a = 74.86, b = 77.45, c = 114.09 Å, and diffract X-rays to 2.6 Å spacing in-house. Determination of the structure of the haem–HemS complex will reveal the molecular basis of haem binding.

  11. Recent development of X-ray crystal structure analysis by a new diffractometer for rapid data collection

    Energy Technology Data Exchange (ETDEWEB)

    Uekusa, Hidehiro [Tokyo Inst. of Tech. (Japan). Faculty of Science

    1995-02-01

    Recently we designed and made a new no-screen Weissenberg camera type diffractometer for rapid data collection to determine the structures of reaction intermediates. The new features of the diffractometer are a {kappa}-type goniometer, two imaging plates for recording and reading the intensity data, and spiral motion reading mechanism. The crystal mounted on a goniometer is aligned automatically and the three-dimensional intensity data were collected within two hours. Using this new diffractometer, we determined the structure of a syn-tricyclooctane derivative. The structure has not been analyzed with the four-circle diffractometer because the molecule easily reacts under X-ray irradiation. (author).

  12. X-Ray Imaging Crystal Spectrometer for Extended X-Ray Sources

    Energy Technology Data Exchange (ETDEWEB)

    Bitter, Manfred L.; Fraekel, Benjamin; Gorman, James L.; Hill, Kenneth W.; Roquemore, Lane A.; Stodiek, Wolfgang; Goeler, Schweickhard von

    1999-05-01

    Spherically or toroidally curved, double focusing crystals are used in a spectrometer for X-ray diagnostics of an extended X-ray source such as a hot plasma produced in a tokamak fusion experiment to provide spatially and temporally resolved data on plasma parameters such as ion temperature, toroidal and poloidal rotation, electron temperature, impurity ion charge-state distributions, and impurity transport. The imaging properties of these spherically or toroidally curved crystals provide both spectrally and spatially resolved X-ray data from the plasma using only one small spherically or toroidally curved crystal, thus eliminating the requirement for a large array of crystal spectrometers and the need to cross-calibrate the various crystals.

  13. Crystallization and preliminary X-ray diffraction analysis of the mitochondrial transcription factor sc-mtTFB from Saccharomyces cerevisiae.

    Science.gov (United States)

    Schubot, F D; Chen, C J; Rose, J P; Wang, B C

    2000-07-01

    Eukaryotic mitochondria contain a distinct mini-chromosome. In yeast, transcription of the mitochondrial genome is mediated by a nuclear-encoded RNA polymerase consisting of a single polypeptide core enzyme and a specificity factor termed sc-mtTFB which bears some similarity to bacterial sigma-factors. sc-mtTFB from Saccharomyces cerevisiae has been cloned, expressed, purified and crystallized. The crystals belong to the monoclinic space group C2, with unit-cell parameters a = 89.7, b = 44.6, c = 98.9 A, beta = 110 degrees. Based on one molecule per asymmetric unit, the solvent content is estimated to be 48%. Small crystals of dimensions 0.01 x 0.05 x 0.13 mm diffract to at least 2.7 A resolution on a rotating-anode X-ray source.

  14. Synthesis, NMR analysis and X-ray crystal structure of 3-(2-naphthoyl)-6,12-diphenyl-3,9-diazatetraasterane

    Science.gov (United States)

    Tan, Hong-bo; Song, Xiu-qing; Yan, Hong; Xin, Hong-xing

    2017-02-01

    Novel 3-(2-naphthoyl)-6,12-diphenyl-3,9-diazatetraasterane (3, Tetraethyl 3-(2-naphthoyl)-6,12-diphenyl-3,9-diazapentacyclo [6.4.0.02,7.04,11.05,10]dodecane-1,5,7,11-tetracarboxylate) was prepared by naphthoylation of 3,9-diazatetraasterane (2). The target compound was isolated and unambiguously confirmed by NMR spectra, high-resolution mass spectrometry, and single-crystal X-ray diffraction analysis. In order to discuss the spatial effects on the NMR of 3 by the naphthoyl group, spectra analysis (1D-NMR and 2D-NMR) of 2 and 3 was conducted in details by the shifts and assignments of signals. Single-crystal X-ray diffraction assists to explain the molecular asymmetry of 3 and elucidates the effects of naphthoyl group on the geometry of the central cage of 3,9-diazatetraasterane.

  15. Crystallization and preliminary X-ray analysis of the glycerol-3-phosphate 1-acyltransferase from squash (Cucurbita moschata).

    Science.gov (United States)

    Turnbull, A P; Rafferty, J B; Sedelnikova, S E; Slabas, A R; Schierer, T P; Kroon, J T; Nishida, I; Murata, N; Simon, J W; Rice, D W

    2001-03-01

    Glycerol-3-phosphate 1-acyltransferase (E.C. 2.3.1.15; G3PAT) catalyses the incorporation of an acyl group from either acyl-acyl carrier proteins (acylACPs) or acylCoAs into the sn-1 position of glycerol 3-phosphate to yield 1-acylglycerol 3-phosphate. Crystals of squash G3PAT have been obtained by the hanging-drop method of vapour diffusion using PEG 4000 as the precipitant. These crystals are most likely to belong to space group P2(1)2(1)2(1), with approximate unit-cell parameters a = 61.1, b = 65.1, c = 103.3 A, alpha = beta = gamma = 90 degrees and a monomer in the asymmetric unit. X-ray diffraction data to 1.9 A resolution have been collected in-house using a MAR 345 imaging-plate system.

  16. Protein preparation, crystallization and preliminary X-ray crystallographic analysis of SMU.961 protein from the caries pathogen Streptococcus mutans.

    Science.gov (United States)

    Gao, Xiong-Zhuo; Li, Lan-Fen; Su, Xiao-Dong; Zhao, XiaoJun; Liang, Yu-He

    2007-10-01

    The smu.961 gene encodes a putative protein of 183 residues in Streptococcus mutans, a major pathogen in human dental caries. The gene was cloned into expression vector pET28a and expressed in a substantial quantity in Escherichia coli strain BL21 (DE3) with a His tag at its N-terminus. The recombinant protein SMU.961 was purified to homogeneity in a two-step procedure consisting of Ni2+-chelating and size-exclusion chromatography. Crystals suitable for X-ray diffraction were obtained by the hanging-drop vapour-diffusion method and diffracted to 2.9 A resolution at beamline I911-3, MAX-II-lab, Sweden. The crystal belonged to space group C2, with unit-cell parameters a = 98.62, b = 73.73, c = 184.73 A, beta = 98.82 degrees.

  17. Cloning, expression, purification, crystallization and preliminary X-ray analysis of EaLsc, a levansucrase from Erwinia amylovora.

    Science.gov (United States)

    Caputi, Lorenzo; Cianci, Michele; Benini, Stefano

    2013-05-01

    The Gram-negative bacterium Erwinia amylovora is a destructive pathogen of Rosaceae. During infection, E. amylovora produces the exopolysaccharide levan, which contributes to the occlusion of plant vessels, causing the wilting of shoots. Levan is a fructose polymer that is synthesized by multifunctional enzymes called levansucrases. The levansucrase from E. amylovora (EaLsc) was heterologously expressed as a GST-fusion protein in Escherichia coli, purified and crystallized after tag removal. The protein crystallized in space group P21212. X-ray diffraction data were acquired to 2.77 Å resolution. The structure of the enzyme was solved by molecular replacement. The asymmetric unit contains eight enzyme molecules, giving a solvent content of 58.74% and a Matthews coefficient of 2.98 Å(3) Da(-1).

  18. Crystallization and preliminary X-ray diffraction analysis of full-length and proteolytically activated pyruvate oxidase from Escherichia coli

    Energy Technology Data Exchange (ETDEWEB)

    Weidner, Annett; Neumann, Piotr; Wille, Georg; Stubbs, Milton T.; Tittmann, Kai, E-mail: kai.tittmann@biochemtech.uni-halle.de [Martin-Luther-Universität Halle-Wittenberg, Naturwissenschaftliche Fakultät I, Institut für Biochemie und Biotechnologie, Kurt-Mothes-Strasse 3, D-06120 Halle (Germany)

    2008-03-01

    The peripheral membrane flavoprotein pyruvate oxidase from E. coli has been crystallized in the full-length form and as a proteolytically activated truncation variant lacking the last 23 amino acids at the C-terminus. The thiamine diphosphate- and flavin-dependent peripheral membrane enzyme pyruvate oxidase from Escherichia coli (EcPOX) has been crystallized in the full-length form and as a proteolytically activated C-terminal truncation variant which lacks the last 23 amino acids (Δ23 EcPOX). Crystals were grown by the hanging-drop vapour-diffusion method using either protamine sulfate (full-length EcPOX) or 2-methyl-2,4-pentanediol (Δ23 EcPOX) as precipitants. Native data sets were collected at a X-ray home source to a resolution of 2.9 Å. The two forms of EcPOX crystallize in different space groups. Whereas full-length EcPOX crystallizes in the tetragonal space group P4{sub 3}2{sub 1}2 with two monomers per asymmetric unit, the crystals of Δ23 EcPOX belong to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1} and contain 12 monomers per asymmetric unit.

  19. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the VP8* carbohydrate-binding protein of the human rotavirus strain Wa

    Energy Technology Data Exchange (ETDEWEB)

    Kraschnefski, Mark J.; Scott, Stacy A. [Institute for Glycomics, Griffith University (Gold Coast Campus), PMB 50 Gold Coast Mail Centre, Queensland 9726 (Australia); Holloway, Gavan; Coulson, Barbara S.; Itzstein, Mark von [Department of Microbiology and Immunology, The University of Melbourne, Victoria 3010 (Australia); Blanchard, Helen, E-mail: h.blanchard@griffith.edu.au [Institute for Glycomics, Griffith University (Gold Coast Campus), PMB 50 Gold Coast Mail Centre, Queensland 9726 (Australia)

    2005-11-01

    The carbohydrate-binding component (VP8*{sub 64–223}) of the human Wa rotavirus spike protein has been overexpressed in E. coli, purified and crystallized in two different crystal forms. X-ray diffraction data have been collected that have enabled determination of the Wa VP8*{sub 64–223} structure by molecular replacement. Rotaviruses exhibit host-specificity and the first crystallographic information on a rotavirus strain that infects humans is reported here. Recognition and attachment to host cells, leading to invasion and infection, is critically linked to the function of the outer capsid spike protein of the rotavirus particle. In some strains the VP8* component of the spike protein is implicated in recognition and binding of sialic-acid-containing cell-surface carbohydrates, thereby enabling infection by the virus. The cloning, expression, purification, crystallization and initial X-ray diffraction analysis of the VP8* core from human Wa rotavirus is reported. Two crystal forms (trigonal P3{sub 2}21 and monoclinic P2{sub 1}) have been obtained and X-ray diffraction data have been collected, enabling determination of the VP8*{sub 64–223} structure by molecular replacement.

  20. Crystallization and preliminary X-ray diffraction analysis of the sialic acid-binding domain (VP8*) of porcine rotavirus strain CRW-8

    Energy Technology Data Exchange (ETDEWEB)

    Scott, Stacy A. [Institute for Glycomics, Griffith University (Gold Coast Campus) PMB 50, Gold Coast Mail Centre, Queensland 9726 (Australia); Holloway, Gavan; Coulson, Barbara S. [Department of Microbiology and Immunology, The University of Melbourne, Victoria 3010 (Australia); Szyczew, Alex J.; Kiefel, Milton J.; Itzstein, Mark von; Blanchard, Helen, E-mail: h.blanchard@griffith.edu.au [Institute for Glycomics, Griffith University (Gold Coast Campus) PMB 50, Gold Coast Mail Centre, Queensland 9726 (Australia)

    2005-06-01

    The sialic acid-binding domain (VP8*) component of the porcine CRW-8 rotavirus spike protein has been overexpressed in E. coli, purified and co-crystallized with an N-acetylneuraminic acid derivative. X-ray diffraction data have been collected to 2.3 Å, which has enabled determination of the structure by molecular replacement. Rotavirus recognition and attachment to host cells involves interaction with the spike protein VP4 that projects outwards from the surface of the virus particle. An integral component of these spikes is the VP8* domain, which is implicated in the direct recognition and binding of sialic acid-containing cell-surface carbohydrates and facilitates subsequent invasion by the virus. The expression, purification, crystallization and preliminary X-ray diffraction analysis of VP8* from porcine CRW-8 rotavirus is reported. Diffraction data have been collected to 2.3 Å resolution, enabling the determination of the VP8* structure by molecular replacement.

  1. Multiplicity factor and diffraction geometry factor for single crystal X-ray diffraction analysis and measurement of phase content in cubic GaN/GaAs(001) epilayers

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    On the basis of integrated intensity of rocking curves, the multiplicity factor and the diffraction geometry factor for single crystal X-ray diffraction (XRD) analysis were proposed and a general formula for calculating the content of mixed phases was obtained. With a multifunction four-circle X-ray double-crystal diffractometer, pole figures of cubic (002), {111} and hexagonal {1010} and reciprocal space mapping were measured to investigate the distributive character of mixed phases and to obtain their multiplicity factors and diffraction geometry factors. The contents of cubic twins and hexagonal inclusions were calculated by the integrated intensities of rocking curves of cubic (002), cubic twin {111}, hexagonal {1010} and {1011}.

  2. Crystallization and preliminary X-ray crystallographic analysis of the tRNA-specific adenosine deaminase from Streptococcus pyogenes

    Energy Technology Data Exchange (ETDEWEB)

    Ku, Min-Je [Functional Proteomics Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seongbuk-gu, Seoul 136-791 (Korea, Republic of); Lee, Won-Ho [Functional Proteomics Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seongbuk-gu, Seoul 136-791 (Korea, Republic of); Biotechnology and Genetic Engineering, Korea University, Seoul 136-701 (Korea, Republic of); Nam, Ki-hyun; Rhee, Kyeong-hee [Biomedical Research Center, Life Science Division, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seongbuk-gu, Seoul 136-791 (Korea, Republic of); Lee, Ki-Seog [Biotechnology and Genetic Engineering, Korea University, Seoul 136-701 (Korea, Republic of); Kim, Eunice EunKyung [Biomedical Research Center, Life Science Division, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seongbuk-gu, Seoul 136-791 (Korea, Republic of); Yu, Myung-Hee [Functional Proteomics Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seongbuk-gu, Seoul 136-791 (Korea, Republic of); Hwang, Kwang Yeon, E-mail: hwangky@kist.re.kr [Biomedical Research Center, Life Science Division, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seongbuk-gu, Seoul 136-791 (Korea, Republic of); Functional Proteomics Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seongbuk-gu, Seoul 136-791 (Korea, Republic of)

    2005-04-01

    The tRNA-specific adenosine deaminase from the pathogenic bacteria S. pyogenes has been overexpressed and crystallized. The tRNA-specific adenosine deaminase from the pathogenic bacteria Streptococcus pyogenes (spTAD) has been overexpressed in Escherichia coli and crystallized in the presence of Zn{sup 2+} ion at 295 K using ammonium sulfate as a precipitant. Flash-cooled crystals of spTAD diffracted to 2.0 Å using 30%(v/v) glycerol as a cryoprotectant. X-ray diffraction data have been collected to 2.0 Å using synchrotron radiation. The crystal belongs to the tetragonal space group P4{sub 2}2{sub 1}2, with unit-cell parameters a = b = 81.042, c = 81.270 Å. The asymmetric unit contains one subunit of spTAD, with a corresponding crystal volume per protein weight (V{sub M}) of 3.3 Å{sup 3} Da{sup −1} and a solvent content of 62.7%.

  3. In situ proteolysis, crystallization and preliminary X-ray diffraction analysis of a VHH that binds listeria internalin B.

    Science.gov (United States)

    Huh, Ian; Gene, Robert; Kumaran, Jyothi; MacKenzie, C Roger; Brooks, Cory L

    2014-11-01

    The variable region of camelid heavy-chain antibodies produces the smallest known antibody fragment with antigen-binding capability (a VHH). The VHH R303 binds internalin B (InlB), a virulence factor expressed by the pathogen Listeria monocytogenes. InlB is critical for initiation of Listeria infection, as it binds a receptor (c-Met) on epithelial cells, triggering the entry of bacteria into host cells. InlB is surface-exposed and is required for virulence, hence a VHH targeting InlB has potential applications for pathogen detection or therapeutic intervention. Here, the expression, purification, crystallization and X-ray diffraction of R303 are reported. Crystals of R303 were obtained following in situ proteolysis with trypsin. Gel filtration and SDS-PAGE revealed that trypsin removed the C-terminal tag region of R303, facilitating crystal formation. Crystals of R303 diffracted to 1.3 Å resolution and belonged to the monoclinic space group P2₁, with unit-cell parameters a=46.4, b=31.2, c=74.8 Å, β=93.8°. The crystals exhibited a Matthews coefficient of 1.95 Å3 Da(-1) with two molecules in the asymmetric unit.

  4. Crystallization and preliminary X-ray diffraction analysis of Sfh3, a member of the Sec14 protein superfamily

    Energy Technology Data Exchange (ETDEWEB)

    Ren, Jihui; Schaaf, Gabriel; Bankaitis, Vytas A.; Ortlund, Eric A.; Pathak, Manish C. (Emory-MED); (UNC)

    2012-03-26

    Sec14 is the major phosphatidylinositol (PtdIns)/phosphatidylcholine (PtdCho) transfer protein in the yeast Saccharomyces cerevisiae and is the founding member of the Sec14 protein superfamily. Recent functional data suggest that Sec14 functions as a nanoreactor for PtdCho-regulated presentation of PtdIns to PtdIns kinase to affect membrane trafficking. Extrapolation of this concept to other members of the Sec14 superfamily suggests a mechanism by which a comprehensive cohort of Sec14-like nanoreactors sense correspondingly diverse pools of lipid metabolites. In turn, metabolic information is translated to signaling circuits driven by phosphoinositide metabolism. Sfh3, one of five Sec14 homologs in yeast, exhibits several interesting functional features, including its unique localization to lipid particles and microsomes. This localization forecasts novel regulatory interfaces between neutral lipid metabolism and phosphoinositide signaling. To launch a detailed structural and functional characterization of Sfh3, the recombinant protein was purified to homogeneity, diffraction-quality crystals were produced and a native X-ray data set was collected to 2.2 {angstrom} resolution. To aid in phasing, SAD X-ray diffraction data were collected to 1.93 {angstrom} resolution from an SeMet-labeled crystal at the Southeast Regional Collaborative Access Team at the Advanced Photon Source. Here, the cloning and purification of Sfh3 and the preliminary diffraction of Sfh3 crystals are reported, enabling structural analyses that are expected to reveal novel principles governing ligand binding and functional specificity for Sec14-superfamily proteins.

  5. Crystallization and preliminary X-ray diffraction analysis of two N-terminal fragments of the DNA-cleavage domain of topoisomerase IV from Staphylococcus aureus

    Energy Technology Data Exchange (ETDEWEB)

    Carr, Stephen B., E-mail: bmbsbc@bmb.leeds.ac.uk [Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT (United Kingdom); Makris, George [Omega Mediation Hellas Ltd, Clinical and Pharma Consulting, 11525 N. Psychiko, Athens (Greece); Phillips, Simon E. V.; Thomas, Christopher D. [Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT (United Kingdom)

    2006-11-01

    The crystallization and data collection of topoisomerase IV from S. aureus is described. Phasing by molecular replacement proved difficult owing to the presence of translational NCS and strategies used to overcome this are discussed. DNA topoisomerase IV removes undesirable topological features from DNA molecules in order to help maintain chromosome stability. Two constructs of 56 and 59 kDa spanning the DNA-cleavage domain of the A subunit of topoisomerase IV from Staphylococcus aureus (termed GrlA56 and GrlA59) have been crystallized. Crystals were grown at 291 K using the sitting-drop vapour-diffusion technique with PEG 3350 as a precipitant. Preliminary X-ray analysis revealed that GrlA56 crystals belong to space group P2{sub 1}, diffract to a resolution of 2.9 Å and possess unit-cell parameters a = 83.6, b = 171.5, c = 87.8 Å, β = 90.1°, while crystals of GrlA59 belong to space group P2{sub 1}2{sub 1}2, with unit-cell parameters a = 41.5, b = 171.89, c = 87.9 Å. These crystals diffract to a resolution of 2.8 Å. This is the first report of the crystallization and preliminary X-ray analysis of the DNA-cleavage domain of a topoisomerase IV from a Gram-positive organism.

  6. Mechanisms for Improved Hygroscopicity of L-Arginine Valproate Revealed by X-Ray Single Crystal Structure Analysis.

    Science.gov (United States)

    Ito, Masataka; Nambu, Kaori; Sakon, Aya; Uekusa, Hidehiro; Yonemochi, Etsuo; Noguchi, Shuji; Terada, Katsuhide

    2017-03-01

    Valproic acid is widely used as an antiepileptic agent. Valproic acid is in liquid phase while sodium valproate is in solid phase at room temperature. Sodium valproate is hard to manufacture because of its hygroscopic and deliquescent properties. To improve these, cocrystal and salt screening for valproic acid was employed in this study. Two solid salt forms, l-arginine valproate and l-lysine valproate, were obtained and characterized. By using dynamic vapor sorption method, the critical relative humidity of sodium valproate, l-arginine valproate, and l-lysine valproate were measured. Critical relative humidity of sodium valproate was 40%, of l-lysine valproate was 60%, and of l-arginine valproate was 70%. Single-crystal X-ray structure determination of l-arginine valproate was employed. l-Lysine valproate was of low diffraction quality, and l-arginine valproate formed a 1:1 salt. Crystal l-arginine valproate has a disorder in the methylene carbon chain that creates 2 conformations. The carboxylate group of valproic acid is connected to the amino group of l-arginine. Crystalline morphologies were calculated from its crystal structure. Adsorption of water molecules to crystal facets was simulated by Material Studio. When comparing adsorption energy per site of these salts, sodium valproate is more capable of adsorption of water molecule than l-arginine valproate.

  7. Protein preparation, crystallization and preliminary X-ray crystallographic analysis of SMU.961 protein from the caries pathogen Streptococcus mutans

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Xiong-Zhuo [Institute for Nanobiomedical Technology and Membrane Biology, West China Hospital, Sichuan University, Chengdu 610065, Sichuan (China); National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871 (China); Li, Lan-Fen; Su, Xiao-Dong [National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871 (China); Zhao, XiaoJun, E-mail: zhaoxj@scu.edu.cn [Institute for Nanobiomedical Technology and Membrane Biology, West China Hospital, Sichuan University, Chengdu 610065, Sichuan (China); Liang, Yu-He, E-mail: zhaoxj@scu.edu.cn [National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871 (China); Institute for Nanobiomedical Technology and Membrane Biology, West China Hospital, Sichuan University, Chengdu 610065, Sichuan (China)

    2007-10-01

    The SMU.961 protein from S. mutans was crystallized and preliminary characterization of the crystals, which diffracted to 2.9 Å resolution, shows them to belong to space group C2. The smu.961 gene encodes a putative protein of 183 residues in Streptococcus mutans, a major pathogen in human dental caries. The gene was cloned into expression vector pET28a and expressed in a substantial quantity in Escherichia coli strain BL21 (DE3) with a His tag at its N-terminus. The recombinant protein SMU.961 was purified to homogeneity in a two-step procedure consisting of Ni{sup 2+}-chelating and size-exclusion chromatography. Crystals suitable for X-ray diffraction were obtained by the hanging-drop vapour-diffusion method and diffracted to 2.9 Å resolution at beamline I911-3, MAX-II-lab, Sweden. The crystal belonged to space group C2, with unit-cell parameters a = 98.62, b = 73.73, c = 184.73 Å, β = 98.82°.

  8. Cloning, expression, purification, crystallization and preliminary X-ray crystallographic analysis of bacterioferritin A from Mycobacterium tuberculosis

    Energy Technology Data Exchange (ETDEWEB)

    Gupta, Vibha [Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021 (India); Gupta, Rakesh K. [Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021 (India); Ram Lal Anand College, University of Delhi, Benito Juarez Road, New Delhi 110021 (India); Khare, Garima [Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021 (India); Salunke, Dinakar M. [National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067 (India); Tyagi, Anil K., E-mail: aniltyagi@south.du.ac.in [Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021 (India)

    2008-05-01

    The cloning, purification and crystallization of a bacterioferritin from M. tuberculosis together with preliminary X-ray characterization of its crystals are reported. Bacterioferritins (Bfrs) comprise a subfamily of the ferritin superfamily of proteins that play an important role in bacterial iron storage and homeostasis. Bacterioferritins differ from ferritins in that they have additional noncovalently bound haem groups. To assess the physiological role of this subfamily of ferritins, a greater understanding of the structural details of bacterioferritins from various sources is required. The gene encoding bacterioferritin A (BfrA) from Mycobacterium tuberculosis was cloned and expressed in Escherichia coli. The recombinant protein product was purified by affinity chromatography on a Strep-Tactin column and crystallized with sodium chloride as a precipitant at pH 8.0 using the vapour-diffusion technique. The crystals diffracted to 2.1 Å resolution and belonged to space group P4{sub 2}, with unit-cell parameters a = 123.0, b = 123.0, c = 174.6 Å.

  9. Crystals x-rays and proteins comprehensive protein crystallography

    CERN Document Server

    Sherwood, Dennis

    2011-01-01

    Information derived from X-ray crystal structures of biological molecules allows us to explain their functions in living organisms and to develop drugs to treat disease. This book describes the principles and practice of X-ray diffraction as a key technique at the forefront of new discoveries in biology and medicine.

  10. Stig Sundell at the bent crystal X-ray spectrometer for the X-ray shift experiment.

    CERN Multimedia

    1976-01-01

    The bent crystal X-ray spectrometer is being used to measure small shifts in the frequencies of X-rays emitted from the lower electron energy levels, in order to learn about the size of the nuclei concerned

  11. Crystallization and X-ray data analysis of the 10 kDa C-terminal lid subdomain from Caenorhabditis elegans Hsp70

    Energy Technology Data Exchange (ETDEWEB)

    Worrall, Liam; Walkinshaw, Malcolm D., E-mail: m.walkinshaw@ed.ac.uk [School of Biological Sciences, University of Edinburgh, The King’s Buildings, Mayfield Road, Edinburgh EH9 3JR,Scotland (United Kingdom)

    2006-09-01

    Crystals of the C-terminal 10 kDa lid subdomain from the C. elegans chaperone Hsp70 have been obtained that diffract X-rays to ∼3.5 Å and belong to space group I2{sub 1}2{sub 1}2{sub 1}. Analysis of X-ray data and initial heavy-atom phasing reveals 24 monomers in the asymmetric unit related by 432 non-crystallographic symmetry. Hsp70 is an important molecular chaperone involved in the regulation of protein folding. Crystals of the C-terminal 10 kDa helical lid domain (residues 542–640) from a Caenorhabditis elegans Hsp70 homologue have been produced that diffract X-rays to ∼3.4 Å. Crystals belong to space group I2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = b = 197, c = 200 Å. The Matthews coefficient, self-rotation function and Patterson map indicate 24 monomers in the asymmetric unit, showing non-crystallographic 432 symmetry. Molecular-replacement studies using the corresponding domain from rat, the only eukaryotic homologue with a known structure, failed and a mercury derivative was obtained. Preliminary MAD phasing using SHELXD and SHARP for location and refinement of the heavy-atom substructure and SOLOMON for density modification produced interpretable maps with a clear protein–solvent boundary. Further density-modification, model-building and refinement are currently under way.

  12. Recent Results with Crystal X-ray Generators

    Science.gov (United States)

    Brownridge, James; Shafroth, Stephen

    1999-11-01

    Thermally stimulated small crystalsfootnote J. D. Brownridge and S. Raboy, J. Appl. Phys. 86, 640 (1999) of LiTaO3 and LiNbO3 (0.1 cm^3) in mtorr environments are viable alternatives to ^55Fe, ^57Co,^109Cd or ^241Am excitation sources in X-ray Fluorescence (XRF) analysis. Several different types of crystal x-ray generators have been built for use in teachingfootnote S.M. Shafroth and J.D. Brownridge, AIP Conference Proceedings 475, 1100 (1998) and research in physics, biology and environmental studies. These XRF sources can be designed to meet safety standards so no license is required.. They can generate characteristic X-rays of most elements at specified intensities. The design, construction and performance of several units will be discussed. Electrons of energies greater than 50 keV and currents of 10 nA or more can be produced for from several minutes to several hours using these crystals. Some unexpected new results will be presented.

  13. Crystallization and preliminary X-ray diffraction analysis of two N-terminal fragments of the DNA-cleavage domain of topoisomerase IV from Staphylococcus aureus.

    Science.gov (United States)

    Carr, Stephen B; Makris, George; Phillips, Simon E V; Thomas, Christopher D

    2006-11-01

    DNA topoisomerase IV removes undesirable topological features from DNA molecules in order to help maintain chromosome stability. Two constructs of 56 and 59 kDa spanning the DNA-cleavage domain of the A subunit of topoisomerase IV from Staphylococcus aureus (termed GrlA56 and GrlA59) have been crystallized. Crystals were grown at 291 K using the sitting-drop vapour-diffusion technique with PEG 3350 as a precipitant. Preliminary X-ray analysis revealed that GrlA56 crystals belong to space group P2(1), diffract to a resolution of 2.9 A and possess unit-cell parameters a = 83.6, b = 171.5, c = 87.8 A, beta = 90.1 degrees, while crystals of GrlA59 belong to space group P2(1)2(1)2, with unit-cell parameters a = 41.5, b = 171.89, c = 87.9 A. These crystals diffract to a resolution of 2.8 A. This is the first report of the crystallization and preliminary X-ray analysis of the DNA-cleavage domain of a topoisomerase IV from a Gram-positive organism.

  14. Crystallization and preliminary X-ray crystallographic analysis of L-arabinose isomerase from thermophilic Geobacillus kaustophilus.

    Science.gov (United States)

    Cao, Thinh-Phat; Choi, Jin Myung; Lee, Sang-Jae; Lee, Yong-Jik; Lee, Sung-Keun; Jun, Youngsoo; Lee, Dong-Woo; Lee, Sung Haeng

    2014-01-01

    L-arabinose isomerase (AI), which catalyzes the isomerization of L-arabinose to L-ribulose, can also convert D-galactose to D-tagatose, a natural sugar replacer, which is of commercial interest in the food and healthcare industries. Intriguingly, mesophilic and thermophilic AIs showed different substrate preferences and metal requirements in catalysis and different thermostabilities. However, the catalytic mechanism of thermophilic AIs still remains unclear. Therefore, thermophilic Geobacillus kaustophilus AI (GKAI) was overexpressed, purified and crystallized, and a preliminary X-ray diffraction data set was obtained. Diffraction data were collected from a GKAI crystal to 2.70 Å resolution. The crystal belonged to the monoclinic space group C2, with unit-cell parameters a = 224.12, b = 152.95, c = 91.28 Å, β = 103.61°. The asymmetric unit contained six molecules, with a calculated Matthews coefficient of 2.25 Å(3) Da(-1) and a solvent content of 45.39%. The three-dimensional structure determination of GKAI is currently in progress by molecular replacement and model building.

  15. Preparation and Crystal Structures of Some AIVB2IIO4 Compounds: Powder X-Ray Diffraction and Rietveld Analysis

    Directory of Open Access Journals (Sweden)

    K. Jeyadheepan

    2014-01-01

    Full Text Available The AIVB2IIO4 compounds such as cadmium tin oxide (Cd2SnO4 or CTO and zinc tin oxide (Zn2SnO4 or ZTO are synthesized by solid state reaction of the subsequent binary oxides. The synthesized powders were analyzed through the powder X-ray diffraction (PXRD. Cell search done on the PXRD patterns shows that the Cd2SnO4 crystallizes in orthorhombic structure with space group Pbam and the cell parameters as a=5.568(2 Å, b=9.894(3 Å, and c=3.193(1 Å and the Zn2SnO4 crystallizes as cubic with the space group Fd3 -m and with the cell parameter a=8.660(2 Å. Rietveld refinement was done on the PXRD patterns to get the crystal structure of the Cd2SnO4 and Zn2SnO4 and to define the site deficiency of atoms which causes the electrical properties of the materials.

  16. Crystallization and X-ray diffraction analysis of the Trp/amber editing site of hepatitis delta virus (+)RNA: a case of rational design

    Energy Technology Data Exchange (ETDEWEB)

    MacElrevey, Celeste; Wedekind, Joseph E., E-mail: joseph-wedekind@urmc.rochester.edu [Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642 (United States)

    2005-12-01

    Well diffracting decamer crystals of the hepatitis delta virus RNA-editing site were prepared, but exhibited merohedral twinning and base averaging owing to duplex symmetry. A longer asymmetric construct that includes additional flanking RNA sequences has been crystallized that does not appear to exhibit these defects. RNA editing by mammalian ADAR1 (Adenosine Deaminase Acting on RNA) is required for the life cycle of the hepatitis delta virus (HDV). Editing extends the single viral open reading frame to yield two protein products of alternate length. ADARs are believed to recognize double-stranded RNA substrates via a ‘structure-based’ readout mechanism. Crystals of 10-mer duplexes representing the HDV RNA-editing site diffracted to 1.35 Å resolution, but suffered from merohedral twinning and averaging of the base registry. Expansion of the construct to include two flanking 3 × 1 internal loops yielded crystals in the primitive tetragonal space group P4{sub 1}2{sub 1}2 or P4{sub 3}2{sub 1}2. X-ray diffraction data were collected to 2.8 Å resolution, revealing a unit cell with parameters a = 62.5, c = 63.5 Å. The crystallization and X-ray analysis of multiple forms of the HDV RNA-editing substrate, encounters with common RNA crystal-growth defects and a strategy to overcome these problems are reported.

  17. Crystallization of the glycogen-binding domain of the AMP-activated protein kinase β subunit and preliminary X-ray analysis

    Energy Technology Data Exchange (ETDEWEB)

    Polekhina, Galina, E-mail: gpolekhina@svi.edu.au; Feil, Susanne C.; Gupta, Abhilasha [St Vincent’s Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065 (Australia); O’Donnell, Paul [Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville 3010 (Australia); Stapleton, David; Parker, Michael W. [St Vincent’s Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065 (Australia)

    2005-01-01

    The glycogen-binding domain of the AMP-activated kinase β subunit has been crystallized in the presence of β-cyclodextrin. The structure has been determined by single isomorphous replacement and threefold averaging using in-house X-ray data collected from selenomethionine-substituted protein. AMP-activated protein kinase (AMPK) is an intracellular energy sensor that regulates metabolism in response to energy demand and supply by adjusting the ATP-generating and ATP-consuming pathways. AMPK potentially plays a critical role in diabetes and obesity as it is known to be activated by metforin and rosiglitazone, drugs used for the treatment of type II diabetes. AMPK is a heterotrimer composed of a catalytic α subunit and two regulatory subunits, β and γ. Mutations in the γ subunit are known to cause glycogen accumulation, leading to cardiac arrhythmias. Recently, a functional glycogen-binding domain (GBD) has been identified in the β subunit. Here, the crystallization of GBD in the presence of β-cyclodextrin is reported together with preliminary X-ray data analysis allowing the determination of the structure by single isomorphous replacement and threefold averaging using in-house X-ray data collected from a selenomethionine-substituted protein.

  18. X-ray Scintillation in Lead Halide Perovskite Crystals

    OpenAIRE

    Birowosuto, M. D.; Cortecchia, D.; Drozdowski, W.; K. Brylew; Łachmański, W.; A. Bruno; Soci, C.

    2016-01-01

    Current technologies for X-ray detection rely on scintillation from expensive inorganic crystals grown at high-temperature, which so far has hindered the development of large-area scintillator arrays. Thanks to the presence of heavy atoms, solution-grown hybrid lead halide perovskite single crystals exhibit short X-ray absorption length and excellent detection efficiency. Here we compare X-ray scintillator characteristics of three-dimensional (3D) MAPbI3 and MAPbBr3 and two-dimensional (2D) (...

  19. Crystallization and preliminary X-ray diffraction analysis of BipD, a virulence factor from Burkholderia pseudomallei

    Energy Technology Data Exchange (ETDEWEB)

    Knight, M. J.; Ruaux, A.; Mikolajek, H.; Erskine, P. T.; Gill, R.; Wood, S. P. [School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX (United Kingdom); Wood, M. [Institute of Animal Health, Division of Environmental Microbiology, Institute for Animal Health, Compton Laboratory, Berkshire RG20 7NN (United Kingdom); Cooper, J. B., E-mail: j.b.cooper@soton.ac.uk [School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX (United Kingdom)

    2006-08-01

    BipD is likely to be a component of a type-III protein secretion system (TTSS) in B. pseudomallei. Native and selenomethionyl-BipD proteins have been expressed and crystals have been obtained which diffract to 2.1 Å. Burkholderia pseudomallei, the causative agent of melioidosis, possesses a protein-secretion apparatus that is similar to those found in Salmonella and Shigella. A major function of these secretion systems is to secrete virulence-associated proteins into target cells of the host organism. The BipD gene of B. pseudomallei encodes a secreted virulence factor that is similar in sequence and most likely functionally analogous to IpaD from Shigella and SipD from Salmonella. Thus, the BipD protein is likely to be a component of a type III protein-secretion system (TTSS) in B. pseudomallei. Proteins in the same class as BipD, such as IpaD and SipD, are thought to act as extracellular chaperones to help the hydrophobic translocator proteins enter the target cell membrane, where they form a pore and might even link the translocon pore with the secretion needle. There is evidence that the translocator proteins also bind an integrin which stimulates actin-mediated insertion of the bacterium into the host-cell membrane. Native BipD has been crystallized in a monoclinic crystal form that diffracts X-rays to 2.5 Å resolution. BipD protein which incorporates selenomethionine (SeMet-BipD) has also been expressed and forms crystals which diffract to a higher resolution of 2.1 Å.

  20. Expression, purification, crystallization and preliminary X-ray analysis of an NADP-dependent glyceraldehyde-3-phosphate dehydrogenase from Helicobacter pylori

    Energy Technology Data Exchange (ETDEWEB)

    Elliott, Paul R.; Evans, Daniel; Greenwood, Jacqueline A.; Moody, Peter C. E., E-mail: pcem1@leicester.ac.uk [Henry Wellcome Laboratories for Structural Biology, Department of Biochemistry, University of Leicester, Leicester LE1 9HN (United Kingdom)

    2008-08-01

    Glyceraldehyde-3-phosphate dehydrogenase A has been cloned, expressed and purified. Apoprotein crystals have been grown which diffracted to 1.75 Å resolution and belonged to space group P2{sub 1}; holo crystals were grown in the presence of NADP, diffracted to 2.6 Å resolution and belonged to space group P3{sub 2}. The classical glycolytic pathway contains an NAD-dependent glyceraldehyde-3-phosphate dehydrogenase, with NADP-dependent forms reserved for photosynthetic organisms and archaea. Here, the cloning, expression, purification, crystallization and preliminary X-ray analysis of an NADP-dependent glyceraldehyde-3-phosphate dehydrogenase from Helicobacter pylori is reported; crystals of the protein were grown both in the presence and the absence of NADP.

  1. Overexpression, crystallization and preliminary X-ray crystallographic analysis of a putative transposase from Thermoplasma acidophilum encoded by the Ta0474 gene

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Ji Yong; Lee, Hyung Ho; Kim, Do Jin; Han, Sang Hee; Kim, Olesya; Kim, Hyoun Sook; Lee, Sang Jae; Suh, Se Won, E-mail: sewonsuh@snu.ac.kr [Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742 (Korea, Republic of)

    2006-11-01

    A putative transposase from T. acidophilum encoded by the Ta0474 gene was crystallized and X-ray diffraction data were collected to 1.78 Å. IS200 transposases, originally identified in Salmonella typhimurium LT2, are present in many bacteria and archaea and are distinct from other groups of transposases. To facilitate further structural comparisons among IS200-like transposases, structural analysis has been initiated of a putative transposase from Thermoplasma acidophilum encoded by the Ta0474 gene. Its 137-residue polypeptide shows high levels of sequence similarity to other members of the IS200 transposase family. The protein was overexpressed in intact form in Escherichia coli and crystallized at 297 K using a reservoir solution consisting of 100 mM Na HEPES pH 7.5 and 20%(v/v) ethanol. X-ray diffraction data were collected to 1.78 Å. The crystals belong to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 65.00, b = 34.07, c = 121.58 Å, α = 90, β = 100.20, γ = 90°. Four monomers, representing two copies of a dimeric molecule, are present in the asymmetric unit, giving a crystal volume per protein weight (V{sub M}) of 2.02 Å{sup 3} Da{sup −1} and a solvent content of 39.2%.

  2. Synthesis, characterization and single crystal x-ray analysis of a complex of iron(II) bis(2,4-dimethylphenyl)dithiophosphate with 4-ethylpyridine

    Science.gov (United States)

    Kumar, Sandeep; Andotra, Savit; Kaur, Mandeep; Gupta, Vivek K.; Kant, Rajni; Pandey, Sushil K.

    2016-09-01

    Complex of iron(II) bis(2,4-dimethylphenyl)dithiophosphate with 4-ethylpyridine [{(2,4- (CH3)2C6H3O)2PS2}2Fe{NC5H4(C2H5)-4}2] is synthesized and characterized by elemental analysis, magnetic moment, IR spectroscopy and single crystal X-ray analysis. Complex crystallizes in the monoclinic sp. gr. P21/ n, Z = 2. Crystal structure consists of mononuclear units with Fe(II) ion chelated by four S atoms of the two diphenyldithiophosphate ligands in bidentate manner. N atoms from two 4-ethylpyridine ligands are axially coordinated to the Fe(II) atom leading to an octahedral geometry.

  3. Crystallization and preliminary X-ray diffraction analysis of myotoxin I, a Lys49-phospholipase A{sub 2} from Bothrops moojeni

    Energy Technology Data Exchange (ETDEWEB)

    Marchi-Salvador, D. P. [Departamento de Física e Biofísica-IB, UNESP, CP 510, CEP 18618-000, Botucatu-SP (Brazil); Silveira, L. B.; Soares, A. M. [Departamento de Biotecnologia, UNAERP, Ribeirão Preto/SP (Brazil); Fontes, M. R. M., E-mail: fontes@ibb.unesp.br [Departamento de Física e Biofísica-IB, UNESP, CP 510, CEP 18618-000, Botucatu-SP (Brazil)

    2005-10-01

    A new myotoxic Lys49-phospholipase from B. moojeni has been crystallized and X-ray diffraction data were collected to 2.18 Å resolution. Preliminary analysis indicates the presence of four molecules in the asymmetric unit, leading to a possible new oligomeric structure for Lys49-PLA{sub 2}s. A new myotoxic Lys49-phospholipase A{sub 2} isolated from Bothrops moojeni snake venom has been crystallized. The crystals diffracted to 2.18 Å resolution using a synchrotron-radiation source and belong to space group C2. The unit-cell parameters are a = 56.8, b = 125.0, c = 64.7 Å, β = 105.5°. Preliminary analysis indicates the presence of four molecules in the asymmetric unit. This may suggest a new quaternary structure for this Lys49-phospholipase A{sub 2} in contrast to the dimeric and monomeric structures solved so far for this class of proteins.

  4. Crystallization and preliminary X-ray analysis of a native human tRNA synthetase whose allelic variants are associated with Charcot–Marie–Tooth disease

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Wei; Schimmel, Paul; Yang, Xiang-Lei, E-mail: xlyang@scripps.edu [Departments of Molecular Biology and Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, BCC-379, 10550 North Torrey Pines Road, La Jolla, CA 92037 (United States)

    2006-12-01

    Crystallization and preliminary X-ray analysis of a native human tRNA synthetase whose allelic variants are associated with Charcot–Marie–Tooth Disease. Glycyl-tRNA synthetase (GlyRS) is one of a group of enzymes that catalyze the synthesis of aminoacyl-tRNAs for translation. Mutations of human and mouse GlyRSs are causally associated with Charcot–Marie–Tooth disease, the most common genetic disorder of the peripheral nervous system. As the first step towards a structure–function analysis of this disease, native human GlyRS was expressed, purified and crystallized. The crystal belonged to space group P4{sub 3}2{sub 1}2 or its enantiomorphic space group P4{sub 1}2{sub 1}2, with unit-cell parameters a = b = 91.74, c = 247.18 Å, and diffracted X-rays to 3.0 Å resolution. The asymmetric unit contained one GlyRS molecule and had a solvent content of 69%.

  5. X-ray diffraction studies of NbTe2 single crystal

    Indian Academy of Sciences (India)

    Neha Bhatt; Rajiv Vaidya; S G Patel; A R Jani

    2004-02-01

    NbTe2 is a member of transition metal dichalcogenide (TMDC) group. Single crystals of niobium ditelluride (NbTe2) have been grown by a chemical vapour transport technique using iodine as transporting agent. The composition of the grown crystals was confirmed on the basis of energy dispersive analysis by X-ray (EDAX) and remaining structural characterization was also accomplished by X-ray diffraction (XRD) studies. Lattice parameters, volume and X-ray density have been carried out for the grown crystals. The particle size for a number of reflections has been calculated using Scherrer’s formula.

  6. Expression, purification, crystallization, and preliminary X-ray crystallographic analysis of OXA-17, an extended-spectrum {beta}-lactamase conferring severe antibiotic resistance

    Energy Technology Data Exchange (ETDEWEB)

    Lee, J. H., E-mail: msgjhlee@mju.ac.kr; Sohn, S. G., E-mail: sgsohn@mju.ac.kr; Jung, H. I., E-mail: jhinumber1@hanmail.net; An, Y. J., E-mail: anyj0120@hanmail.net; Lee, S. H., E-mail: sangheelee@mju.ac.kr [Myongji University, Drug Resistance Proteomics Laboratory, Department of Biological Sciences (Korea, Republic of)

    2013-07-15

    OXA-17, an extended-spectrum {beta}-lactamase (ESBL) conferring severe antibiotic resistance, hydrolytically inactivates {beta}-lactam antibiotics, inducing a lack of eradication of pathogenic bacteria by oxyimino {beta}-lactams and not helping hospital infection control. Thus, the enzyme is a potential target for developing antimicrobial agents against pathogens producing ESBLs. OXA-17 was purified and crystallized at 298 K. X-ray diffraction data from OXA-17 crystal have been collected to 1.85 A resolution using synchrotron radiation. The crystal of OXA-17 belongs to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 48.37, b = 101.12, and c = 126.07 A. Analysis of the packing density shows that the asymmetric unit probably contains two molecules with a solvent content of 54.6%.

  7. Purification, crystallization and preliminary X-ray diffraction analysis of the CBS-domain pair from the Methanococcus jannaschii protein MJ0100

    Science.gov (United States)

    Lucas, María; Kortazar, Danel; Astigarraga, Egoitz; Fernández, José A.; Mato, Jose M.; Martínez-Chantar, María Luz; Martínez-Cruz, Luis Alfonso

    2008-01-01

    CBS domains are small protein motifs consisting of a three-stranded β-sheet and two α-helices that are present in proteins of all kingdoms of life and in proteins with completely different functions. Several genetic diseases in humans have been associated with mutations in their sequence, which has made them promising targets for rational drug design. The C-terminal domain of the Methanococcus jannaschii protein MJ0100 includes a CBS-domain pair and has been overexpressed, purified and crystallized. Crystals of selenomethionine-substituted (SeMet) protein were also grown. The space group of both the native and SeMet crystals was determined to be orthorhombic P212121, with unit-cell parameters a = 80.9, b = 119.5, c = 173.3 Å. Preliminary analysis of the X-ray data indicated that there were eight molecules per asymmetric unit in both cases. PMID:18931440

  8. Expression, purification, crystallization, and preliminary X-ray crystallographic analysis of OXA-17, an extended-spectrum β-lactamase conferring severe antibiotic resistance

    Science.gov (United States)

    Lee, J. H.; Sohn, S. G.; Jung, H. I.; An, Y. J.; Lee, S. H.

    2013-07-01

    OXA-17, an extended-spectrum β-lactamase (ESBL) conferring severe antibiotic resistance, hydrolytically inactivates β-lactam antibiotics, inducing a lack of eradication of pathogenic bacteria by oxyimino β-lactams and not helping hospital infection control. Thus, the enzyme is a potential target for developing antimicrobial agents against pathogens producing ESBLs. OXA-17 was purified and crystallized at 298 K. X-ray diffraction data from OXA-17 crystal have been collected to 1.85 Å resolution using synchrotron radiation. The crystal of OXA-17 belongs to space group P212121, with unit-cell parameters a = 48.37, b = 101.12, and c = 126.07 Å. Analysis of the packing density shows that the asymmetric unit probably contains two molecules with a solvent content of 54.6%.

  9. Crystallization and preliminary X-ray diffraction analysis of the Fab fragment of WO2, an antibody specific for the Aβ peptides associated with Alzheimer’s disease

    Energy Technology Data Exchange (ETDEWEB)

    Wun, Kwok S. [Biota Structural Biology Laboratory and Centre for Structural Neurobiology, St Vincent’s Institute of Medical Research, 41 Victoria Parade, Fitzroy, Victoria 3065 (Australia); Miles, Luke A. [Biota Structural Biology Laboratory and Centre for Structural Neurobiology, St Vincent’s Institute of Medical Research, 41 Victoria Parade, Fitzroy, Victoria 3065 (Australia); Department of Chemical and Biomolecular Engineering, The University of Melbourne, Victoria 3010 (Australia); Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010 (Australia); Crespi, Gabriela A. N. [Biota Structural Biology Laboratory and Centre for Structural Neurobiology, St Vincent’s Institute of Medical Research, 41 Victoria Parade, Fitzroy, Victoria 3065 (Australia); Wycherley, Kaye [WEHI Biotechnology Centre, La Trobe R& D Park, Bundoora, Victoria 3086 (Australia); Ascher, David B. [Biota Structural Biology Laboratory and Centre for Structural Neurobiology, St Vincent’s Institute of Medical Research, 41 Victoria Parade, Fitzroy, Victoria 3065 (Australia); Barnham, Kevin J.; Cappai, Roberto [Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010 (Australia); Department of Pathology, The University of Melbourne, Victoria 3010 (Australia); The Mental Health Research Institute of Victoria, Parkville, Victoria 3052 (Australia); Beyreuther, Konrad [ZMBH, University of Heidelberg, Heidelberg (Germany); Masters, Colin L. [Department of Pathology, The University of Melbourne, Victoria 3010 (Australia); The Mental Health Research Institute of Victoria, Parkville, Victoria 3052 (Australia); Parker, Michael W. [Biota Structural Biology Laboratory and Centre for Structural Neurobiology, St Vincent’s Institute of Medical Research, 41 Victoria Parade, Fitzroy, Victoria 3065 (Australia); Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010 (Australia); McKinstry, William J., E-mail: wjmckinstry@hotmail.com [Biota Structural Biology Laboratory and Centre for Structural Neurobiology, St Vincent’s Institute of Medical Research, 41 Victoria Parade, Fitzroy, Victoria 3065 (Australia); Department of Medicine (St Vincent’s Hospital), The University of Melbourne, 41 Victoria Parade, Fitzroy 3065 (Australia)

    2008-05-01

    Crystallization and X-ray diffraction data collection of the Fab fragment of the monoclonal antibody WO2 in the absence or presence of amyloid β peptides associated with Alzheimer’s disease are reported. The murine monoclonal antibody WO2 specifically binds the N-terminal region of the amyloid β peptide (Aβ) associated with Alzheimer’s disease. This region of Aβ has been shown to be the immunodominant B-cell epitope of the peptide and hence is considered to be a basis for the development of immunotherapeutic strategies against this prevalent cause of dementia. Structural studies have been undertaken in order to characterize the molecular basis for antibody recognition of this important epitope. Here, details of the crystallization and X-ray analysis of the Fab fragment of the unliganded WO2 antibody in two crystal forms and of the complexes that it forms with the truncated Aβ peptides Aβ{sub 1–16} and Aβ{sub 1–28} are presented. These crystals were all obtained using the hanging-drop vapour-diffusion method at 295 K. Crystals of WO2 Fab were grown in polyethylene glycol solutions containing ZnSO{sub 4}; they belonged to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1} and diffracted to 1.6 Å resolution. The complexes of WO2 Fab with either Aβ{sub 1–@}@{sub 16} or Aβ{sub 1–28} were cocrystallized from polyethylene glycol solutions. These two complex crystals grew in the same space group, P2{sub 1}2{sub 1}2{sub 1}, and diffracted to 1.6 Å resolution. A second crystal form of WO2 Fab was grown in the presence of the sparingly soluble Aβ{sub 1–42} in PEG 550 MME. This second form belonged to space group P2{sub 1} and diffracted to 1.9 Å resolution.

  10. Crystallization and preliminary X-ray diffraction analysis of mouse galectin-4 N-terminal carbohydrate recognition domain in complex with lactose.

    Science.gov (United States)

    Krejciríková, Veronika; Fábry, Milan; Marková, Vladimíra; Malý, Petr; Rezácová, Pavlína; Brynda, Jirí

    2008-07-01

    Galectin-4 is thought to play a role in the process of tumour conversion of cells of the alimentary tract and the breast tissue; however, its exact function remains unknown. With the aim of elucidating the structural basis of mouse galectin-4 (mGal-4) binding specificity, we have undertaken X-ray analysis of the N-terminal domain, CRD1, of mGal-4 in complex with lactose (the basic building block of known galectin-4 carbohydrate ligands). Crystals of CRD1 in complex with lactose were obtained using vapour-diffusion techniques. The crystals belong to tetragonal space group P42(1)2 with unit-cell parameters a = 91.1, b = 91.16, c = 57.10 A and preliminary X-ray diffraction data were collected to 3.2 A resolution. An optimized crystallization procedure and cryocooling protocol allowed us to extend resolution to 2.1 A. Structure refinement is currently under way; the initial electron-density maps clearly show non-protein electron density in the vicinity of the carbohydrate binding site, indicating the presence of one lactose molecule. The structure will help to improve understanding of the binding specificity and function of the potential colon cancer marker galectin-4.

  11. Locating and Visualizing Crystals for X-Ray Diffraction Experiments.

    Science.gov (United States)

    Becker, Michael; Kissick, David J; Ogata, Craig M

    2017-01-01

    Macromolecular crystallography has advanced from using macroscopic crystals, which might be >1 mm on a side, to crystals that are essentially invisible to the naked eye, or even under a standard laboratory microscope. As crystallography requires recognizing crystals when they are produced, and then placing them in an X-ray, electron, or neutron beam, this provides challenges, particularly in the case of advanced X-ray sources, where beams have very small cross sections and crystals may be vanishingly small. Methods for visualizing crystals are reviewed here, and examples of different types of cases are presented, including: standard crystals, crystals grown in mesophase, in situ crystallography, and crystals grown for X-ray Free Electron Laser or Micro Electron Diffraction experiments. As most techniques have limitations, it is desirable to have a range of complementary techniques available to identify and locate crystals. Ideally, a given technique should not cause sample damage, but sometimes it is necessary to use techniques where damage can only be minimized. For extreme circumstances, the act of probing location may be coincident with collecting X-ray diffraction data. Future challenges and directions are also discussed.

  12. Crystallization and preliminary X-ray diffraction analysis on the homing endonuclease I-Dmo-I in complex with its target DNA

    Energy Technology Data Exchange (ETDEWEB)

    Redondo, Pilar [Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Centre (CNIO), c/Melchor Fdez. Almagro 3, 28029 Madrid (Spain); Prieto, Jesús; Ramos, Elena; Blanco, Francisco J. [NMR Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Centre (CNIO), c/Melchor Fdez. Almagro 3, 28029 Madrid (Spain); Montoya, Guillermo, E-mail: gmontoya@cnio.es [Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Centre (CNIO), c/Melchor Fdez. Almagro 3, 28029 Madrid (Spain)

    2007-12-01

    I-Dmo-I is a well characterized homing endonuclease from the archaeon Desulfurococcus mobilis. The enzyme was cloned and overexpressed in Escherichia coli. Crystallization experiments of I-Dmo-I in complex with its DNA target in the presence of Ca{sup 2+} and Mg{sup 2+} yielded crystals that were suitable for X-ray diffraction analysis. Homing endonucleases are highly specific DNA-cleaving enzymes that recognize long stretches of base pairs. The availability of these enzymes has opened novel perspectives for genome engineering in a wide range of fields, including gene therapy, by taking advantage of the homologous gene-targeting enhancement induced by a double-strand break. I-Dmo-I is a well characterized homing endonuclease from the archaeon Desulfurococcus mobilis. The enzyme was cloned and overexpressed in Escherichia coli. Crystallization experiments of I-Dmo-I in complex with its DNA target in the presence of Ca{sup 2+} and Mg{sup 2+} yielded crystals that were suitable for X-ray diffraction analysis. The crystals belonged to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 106.75, b = 70.18, c = 106.85 Å, α = γ = 90, β = 119.93°. The self-rotation function and the Matthews coefficient suggested the presence of three protein–DNA complexes per asymmetric unit. The crystals diffracted to a resolution limit of 2.6 Å using synchrotron radiation at the Swiss Light Source (SLS) and the European Synchrotron Radiation Facility (ESRF)

  13. Femtosecond X-ray diffraction from two-dimensional protein crystals.

    Science.gov (United States)

    Frank, Matthias; Carlson, David B; Hunter, Mark S; Williams, Garth J; Messerschmidt, Marc; Zatsepin, Nadia A; Barty, Anton; Benner, W Henry; Chu, Kaiqin; Graf, Alexander T; Hau-Riege, Stefan P; Kirian, Richard A; Padeste, Celestino; Pardini, Tommaso; Pedrini, Bill; Segelke, Brent; Seibert, M Marvin; Spence, John C H; Tsai, Ching-Ju; Lane, Stephen M; Li, Xiao-Dan; Schertler, Gebhard; Boutet, Sebastien; Coleman, Matthew; Evans, James E

    2014-03-01

    X-ray diffraction patterns from two-dimensional (2-D) protein crystals obtained using femtosecond X-ray pulses from an X-ray free-electron laser (XFEL) are presented. To date, it has not been possible to acquire transmission X-ray diffraction patterns from individual 2-D protein crystals due to radiation damage. However, the intense and ultrafast pulses generated by an XFEL permit a new method of collecting diffraction data before the sample is destroyed. Utilizing a diffract-before-destroy approach at the Linac Coherent Light Source, Bragg diffraction was acquired to better than 8.5 Å resolution for two different 2-D protein crystal samples each less than 10 nm thick and maintained at room temperature. These proof-of-principle results show promise for structural analysis of both soluble and membrane proteins arranged as 2-D crystals without requiring cryogenic conditions or the formation of three-dimensional crystals.

  14. X-ray scattering from surfaces of organic crystals

    DEFF Research Database (Denmark)

    Gidalevitz, D.; Feidenhans'l, R.; Smilgies, D.-M.

    1997-01-01

    X-ray scattering experiments have been performed on the surfaces of organic crystals. The (010) cleavage planes of beta-alanine and alpha-glycine were investigated, and both specular and off-specular crystal truncation rods were measured. This allowed a determination of the molecular layering...

  15. X-Ray structural investigation of VAS-393 crystals

    CERN Document Server

    Martirosian, A H; Harurtjunian, V S

    2001-01-01

    X-ray structural study of VAS-393 crystals was performed. Investigations were carried out with the use of the Weissenberg rotating and powder (employing the Bjornstrem diagrams) methods. The lattice constants ''c'' and ''a''are calculated. The crystal is shown to belong to the trigonal syngony (medium category)

  16. A short working distance multiple crystal x-ray spectrometer

    Science.gov (United States)

    Dickinson, B.; Seidler, G.T.; Webb, Z.W.; Bradley, J.A.; Nagle, K.P.; Heald, S.M.; Gordon, R.A.; Chou, I.-Ming

    2008-01-01

    For x-ray spot sizes of a few tens of microns or smaller, a millimeter-sized flat analyzer crystal placed ???1 cm from the sample will exhibit high energy resolution while subtending a collection solid angle comparable to that of a typical spherically bent crystal analyzer (SBCA) at much larger working distances. Based on this observation and a nonfocusing geometry for the analyzer optic, we have constructed and tested a short working distance (SWD) multicrystal x-ray spectrometer. This prototype instrument has a maximum effective collection solid angle of 0.14 sr, comparable to that of 17 SBCA at 1 m working distance. We find good agreement with prior work for measurements of the Mn K?? x-ray emission and resonant inelastic x-ray scattering for MnO, and also for measurements of the x-ray absorption near-edge structure for Dy metal using L??2 partial-fluorescence yield detection. We discuss future applications at third- and fourth-generation light sources. For concentrated samples, the extremely large collection angle of SWD spectrometers will permit collection of high-resolution x-ray emission spectra with a single pulse of the Linac Coherent Light Source. The range of applications of SWD spectrometers and traditional multi-SBCA instruments has some overlap, but also is significantly complementary. ?? 2008 American Institute of Physics.

  17. Crystallization and preliminary X-ray analysis of monalysin, a novel β-pore-forming toxin from the entomopathogen Pseudomonas entomophila.

    Science.gov (United States)

    Blemont, Maryline; Vincentelli, Renaud; Kellenberger, Christine; Opota, Onya; Lemaitre, Bruno; Roussel, Alain; Leone, Philippe

    2013-08-01

    Monalysin was recently described as a novel pore-forming toxin (PFT) secreted by the Drosophila pathogen Pseudomonas entomophila. Recombinant monalysin is multimeric in solution, whereas PFTs are supposed to be monomeric until target membrane association. Monalysin crystals were obtained by the hanging-drop vapour-diffusion method using PEG 8000 as precipitant. Preliminary X-ray diffraction analysis revealed that monalysin crystals belonged to the monoclinic space group C2, with unit-cell parameters a = 162.4, b = 146.2, c = 144.4 Å, β = 122.8°, and diffracted to 2.85 Å resolution using synchrotron radiation. Patterson self-rotation analysis and Matthews coefficient calculation indicate that the asymmetric unit contains nine copies of monalysin. Heavy-atom derivative data were collected and a Ta6Br14 cluster derivative data set confirmed the presence of ninefold noncrystallographic symmetry.

  18. X-ray Scintillation in Lead Halide Perovskite Crystals

    CERN Document Server

    Birowosuto, M D; Drozdowski, W; Brylew, K; Lachmanski, W; Bruno, A; Soci, C

    2016-01-01

    Current technologies for X-ray detection rely on scintillation from expensive inorganic crystals grown at high-temperature, which so far has hindered the development of large-area scintillator arrays. Thanks to the presence of heavy atoms, solution-grown hybrid lead halide perovskite single crystals exhibit short X-ray absorption length and excellent detection efficiency. Here we compare X-ray scintillator characteristics of three-dimensional (3D) MAPbI3 and MAPbBr3 and two-dimensional (2D) (EDBE)PbCl4 hybrid perovskite crystals. X-ray excited thermoluminescence measurements indicate the absence of deep traps and a very small density of shallow trap states, which lessens after-glow effects. All perovskite single crystals exhibit high X-ray excited luminescence yields of >120,000 photons/MeV at low temperature. Although thermal quenching is significant at room temperature, the large exciton binding energy of 2D (EDBE)PbCl4 significantly reduces thermal effects compared to 3D perovskites, and moderate light yie...

  19. X-ray Scintillation in Lead Halide Perovskite Crystals

    Science.gov (United States)

    Birowosuto, M. D.; Cortecchia, D.; Drozdowski, W.; Brylew, K.; Lachmanski, W.; Bruno, A.; Soci, C.

    2016-11-01

    Current technologies for X-ray detection rely on scintillation from expensive inorganic crystals grown at high-temperature, which so far has hindered the development of large-area scintillator arrays. Thanks to the presence of heavy atoms, solution-grown hybrid lead halide perovskite single crystals exhibit short X-ray absorption length and excellent detection efficiency. Here we compare X-ray scintillator characteristics of three-dimensional (3D) MAPbI3 and MAPbBr3 and two-dimensional (2D) (EDBE)PbCl4 hybrid perovskite crystals. X-ray excited thermoluminescence measurements indicate the absence of deep traps and a very small density of shallow trap states, which lessens after-glow effects. All perovskite single crystals exhibit high X-ray excited luminescence yields of >120,000 photons/MeV at low temperature. Although thermal quenching is significant at room temperature, the large exciton binding energy of 2D (EDBE)PbCl4 significantly reduces thermal effects compared to 3D perovskites, and moderate light yield of 9,000 photons/MeV can be achieved even at room temperature. This highlights the potential of 2D metal halide perovskites for large-area and low-cost scintillator devices for medical, security and scientific applications.

  20. Crystallization and preliminary X-ray diffraction analysis of L-threonine dehydrogenase (TDH) from the hyperthermophilic archaeon Thermococcus kodakaraensis.

    Science.gov (United States)

    Bowyer, A; Mikolajek, H; Wright, J N; Coker, A; Erskine, P T; Cooper, J B; Bashir, Q; Rashid, N; Jamil, F; Akhtar, M

    2008-09-01

    The enzyme L-threonine dehydrogenase catalyses the NAD(+)-dependent conversion of L-threonine to 2-amino-3-ketobutyrate, which is the first reaction of a two-step biochemical pathway involved in the metabolism of threonine to glycine. Here, the crystallization and preliminary crystallographic analysis of L-threonine dehydrogenase (Tk-TDH) from the hyperthermophilic organism Thermococcus kodakaraensis KOD1 is reported. This threonine dehydrogenase consists of 350 amino acids, with a molecular weight of 38 kDa, and was prepared using an Escherichia coli expression system. The purified native protein was crystallized using the hanging-drop vapour-diffusion method and crystals grew in the tetragonal space group P4(3)2(1)2, with unit-cell parameters a = b = 124.5, c = 271.1 A. Diffraction data were collected to 2.6 A resolution and preliminary analysis indicates that there are four molecules in the asymmetric unit of the crystal.

  1. Crystallization and preliminary X-ray diffraction analysis of mouse galectin-4 N-terminal carbohydrate recognition domain in complex with lactose

    Energy Technology Data Exchange (ETDEWEB)

    Krejčiříková, Veronika; Fábry, Milan; Marková, Vladimíra; Malý, Petr [Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 37 Praha 6 (Czech Republic); Řezáčová, Pavlína; Brynda, Jiří, E-mail: brynda@img.cas.cz [Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 37 Praha 6 (Czech Republic); Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6 (Czech Republic)

    2008-07-01

    Mouse galectin-4 carbohydrate binding domain was overexpressed in E. coli and crystallized in the presence of lactose. The crystals belong to tetragonal space group P42{sub 1}2 and diffraction data were collected to 2.1 Å resolution. Galectin-4 is thought to play a role in the process of tumour conversion of cells of the alimentary tract and the breast tissue; however, its exact function remains unknown. With the aim of elucidating the structural basis of mouse galectin-4 (mGal-4) binding specificity, we have undertaken X-ray analysis of the N-terminal domain, CRD1, of mGal-4 in complex with lactose (the basic building block of known galectin-4 carbohydrate ligands). Crystals of CRD1 in complex with lactose were obtained using vapour-diffusion techniques. The crystals belong to tetragonal space group P42{sub 1}2 with unit-cell parameters a = 91.1, b = 91.16, c = 57.10 Å and preliminary X-ray diffraction data were collected to 3.2 Å resolution. An optimized crystallization procedure and cryocooling protocol allowed us to extend resolution to 2.1 Å. Structure refinement is currently under way; the initial electron-density maps clearly show non-protein electron density in the vicinity of the carbohydrate binding site, indicating the presence of one lactose molecule. The structure will help to improve understanding of the binding specificity and function of the potential colon cancer marker galectin-4.

  2. Effect of framework and extra-framework cations substitutions on the zeolite structure: Single-crystal X-ray diffraction analysis of analcime and wairakite solid solutions

    Science.gov (United States)

    Sugano, N.; Kyono, A.

    2015-12-01

    There are a large number of natural and synthetic zeolites having a microporous structure, which is generally composed of Si/AlO4 three-dimensional framework. Analcime, NaAlSi2O6·H2O, is one of the most common naturally occurring zeolites. It forms a variety of solid solutions with wairakite, (Ca,Na2)Al2Si4O12·2H2O, pollucite (CsAlSi2O6·nH2O), and hsianghualite (Ca3Li2Be3Si3O12·F2). This study aimed to clarify structural variations in the solid solution between analcime and wairakite. Single crystals with compositions between analcime and wairakite were synthesized using hydrothermal synthesis method. Aluminium sulfate and sodium metasilicate nonahydrate gelled with distilled water were heated for 24 hours under 200 °C. The hydrothermally synthesized crystalline materials were analyzed by scanning electron microscope (SEM). SEM images showed that the grown single crystals exhibited euhedral trapezohedron shape up to 400μm in size. The effect of the cations substitution on the structural variation was examined by single-crystal X-ray diffraction analysis and electron probe micro-analyser (EPMA). Structure refinements based on the single-crystal X-ray diffraction data exhibited that crystal structures between analcime and wairakite belong to the cubic Ia-3d and kept approximately unchanged. Lattice parameter was monotonously reduced from 13.713 (1) Å to 13.650 (1) Å as a function of Ca concentration. In addition, the lattice parameter was also varied with Si/Al framework cation ratio. The contraction of the 6-membered oxygen rings was closely associated with exchanged cations and substituted framework cations. This study indicates that a geometry of micro-porous zeolite structure is significantly influenced by substitution of not only extra-framework cations but framework cations.

  3. Overexpression, purification, crystallization and preliminary X-ray analysis of Rv2780 from Mycobacterium tuberculosis H37Rv

    Energy Technology Data Exchange (ETDEWEB)

    Tripathi, Sarvind Mani; Ramachandran, Ravishankar, E-mail: r-ravishankar@cdri.res.in [Molecular and Structural Biology Division, Central Drug Research Institute, PO Box 173, Chattar Manzil, Mahatma Gandhi Marg, Lucknow 226001 (India)

    2008-05-01

    Rv2780, an alanine dehydrogenase from M. tuberculosis, has been crystallized in apo and NAD/pyruvate-bound forms. Preliminary crystallographic analysis shows that there is a hexamer and trimer in the asymmetric units of the apo and ternary complex forms, respectively. Rv2780, an alanine dehydrogenase from Mycobacterium tuberculosis (MtAlaDH), catalyzes the NAD-dependent interconversion of alanine and pyruvate. Alanine dehydrogenase is released into the culture medium in substantial amounts by virulent strains of mycobacteria and is not found in the vaccine strain of tuberculosis. Crystals of recombinant MtAlaDH were grown from 2 M ammonium sulfate solution at ∼12 mg ml{sup −1} protein concentration in two crystal forms which occur in the presence and absence of NAD/pyruvate, respectively. Diffraction data extending to 2.6 Å were collected at room temperature from both apo and ternary complex crystals. Crystals of the apoenzyme have unit-cell parameters a = 173.89, b = 127.07, c = 135.95 Å. They are rod-like in shape and belong to space group C2. They contain a hexamer in the asymmetric unit. Crystals of the ternary complex belong to space group P4{sub 3}2{sub 1}2 and have unit-cell parameters a = b = 88.99, c = 373.85 Å. There are three subunits in the asymmetric unit of the holoenzyme crystals.

  4. A 1:1 pharmaceutical cocrystal of myricetin in combination with uncommon piracetam conformer: X-ray single crystal analysis and mechanochemical synthesis

    Science.gov (United States)

    Sowa, Michał; Ślepokura, Katarzyna; Matczak-Jon, Ewa

    2014-01-01

    Combination of two Active Pharmaceutical Ingredients, myricetin and piracetam, yields a 1:1 cocrystal characterized by X-ray single-crystal and powder diffraction, Raman spectroscopy, 1H NMR, thermal analysis (DSC and TG-DTA) methods. Constituents of the cocrystalline phase were also investigated in terms of Hirshfeld surfaces. Compounds in their neutral forms cocrystallize in the Pna21 space group of orthorhombic system. Notably, piracetam adopts an uncommon conformation, not encountered in its cocrystals previously described. In the crystal lattice, a three-dimensional hydrogen-bonded network is observed, including formation of a 2D molecular scaffolding motif. A scale-up procedure is readily available with use of solvent-drop grinding method, in which application of a variety of common solvents leads to formation of the cocrystal, as confirmed by XRPD and Raman spectroscopy.

  5. Two crystal x-ray spectrometers for OMEGA experiments

    Science.gov (United States)

    Reverdin, C.; Casner, A.; Girard, F.; Lecherbourg, L.; Loupias, B.; Tassin, V.; Philippe, F.

    2016-11-01

    Two x-ray spectrometers have been built for x-ray spectroscopy of laser-produced plasmas on OMEGA at the Laboratory for Laser Energetics (LLE) by Commissariat a ̀ l'Energie Atomique et aux énergies alternatives (CEA). The accessible photon energy range is from 1.5 to 20 keV. The first spectrometer, called X-ray CEA Crystal Spectrometer with a Charge-Injection Device (XCCS-CID), records three spectra with three crystals coupled to a time integrated CID camera. The second one, called X-ray CEA Crystal Spectrometer (XCCS) with a framing camera, is time resolved and records four spectra with two crystals on the four frames of a framing camera. Cylindrical crystals are used in Johan geometry. Each spectrometer is positioned with a ten-inch manipulator inside the OMEGA target chamber. In each experiment, after choosing a spectral window, a specific configuration is designed and concave crystals are precisely positioned on a board with angled wedges and spacers. Slits on snouts enable 1D spatial resolution to distinguish spectra emitted from different parts of the target.

  6. Dynamic X-ray diffraction sampling for protein crystal positioning.

    Science.gov (United States)

    Scarborough, Nicole M; Godaliyadda, G M Dilshan P; Ye, Dong Hye; Kissick, David J; Zhang, Shijie; Newman, Justin A; Sheedlo, Michael J; Chowdhury, Azhad U; Fischetti, Robert F; Das, Chittaranjan; Buzzard, Gregery T; Bouman, Charles A; Simpson, Garth J

    2017-01-01

    A sparse supervised learning approach for dynamic sampling (SLADS) is described for dose reduction in diffraction-based protein crystal positioning. Crystal centering is typically a prerequisite for macromolecular diffraction at synchrotron facilities, with X-ray diffraction mapping growing in popularity as a mechanism for localization. In X-ray raster scanning, diffraction is used to identify the crystal positions based on the detection of Bragg-like peaks in the scattering patterns; however, this additional X-ray exposure may result in detectable damage to the crystal prior to data collection. Dynamic sampling, in which preceding measurements inform the next most information-rich location to probe for image reconstruction, significantly reduced the X-ray dose experienced by protein crystals during positioning by diffraction raster scanning. The SLADS algorithm implemented herein is designed for single-pixel measurements and can select a new location to measure. In each step of SLADS, the algorithm selects the pixel, which, when measured, maximizes the expected reduction in distortion given previous measurements. Ground-truth diffraction data were obtained for a 5 µm-diameter beam and SLADS reconstructed the image sampling 31% of the total volume and only 9% of the interior of the crystal greatly reducing the X-ray dosage on the crystal. Using in situ two-photon-excited fluorescence microscopy measurements as a surrogate for diffraction imaging with a 1 µm-diameter beam, the SLADS algorithm enabled image reconstruction from a 7% sampling of the total volume and 12% sampling of the interior of the crystal. When implemented into the beamline at Argonne National Laboratory, without ground-truth images, an acceptable reconstruction was obtained with 3% of the image sampled and approximately 5% of the crystal. The incorporation of SLADS into X-ray diffraction acquisitions has the potential to significantly minimize the impact of X-ray exposure on the crystal by

  7. Recombinant expression, purification, crystallization and preliminary X-ray diffraction analysis of Haemophilus influenzae BamD and BamCD complex

    Science.gov (United States)

    Lei, Jintang; Cai, Xun; Ma, Xiaodan; Zhang, Li; Li, Yuwen; Dong, Xue; St Geme, Joseph; Meng, Guoyu

    2015-01-01

    The Bam machinery, which is highly conserved from bacteria to humans, is well recognized as the apparatus responsible for the insertion and folding of most outer membrane proteins in Gram-negative bacteria. In Escherichia coli, the Bam machinery consists of five components (i.e. BamA, BamB, BamC, BamD and BamE). In comparison, there are only four partners in Haemophilus influenzae: a BamB homologue is not found in its genome. In this study, the recombinant expression, purification, crystallization and preliminary X-ray diffraction analysis of H. influenzae BamD and BamCD complex are reported. The genes encoding BamC and BamD were cloned into a pET vector and expressed in E. coli. Affinity, ion-exchange and gel-filtration chromatography were used to obtain high-purity protein for further crystallo­graphic characterization. Using the hanging-drop vapour-diffusion technique, BamD and BamCD protein crystals of suitable size were obtained using protein concentrations of 70 and 50 mg ml−1, respectively. Preliminary X-ray diffraction analysis showed that the BamD crystals diffracted to 4.0 Å resolution and belonged to space group P212121, with unit-cell parameters a = 54.5, b = 130.5, c = 154.7 Å. The BamCD crystals diffracted to 3.8 Å resolution and belonged to space group I212121, with unit-cell parameters a = 101.6, b = 114.1, c = 234.9 Å. PMID:25664802

  8. Ultrafast x-ray diffraction of laser-irradiated crystals

    Science.gov (United States)

    Heimann, P. A.; Larsson, J.; Chang, Z.; Lindenberg, A.; Schuck, P. J.; Judd, E.; Padmore, H. A.; Bucksbaum, P. H.; Lee, R. W.; Murnane, M.; Kapteyn, H.; Wark, J. S.; Falcone, R. W.

    1997-07-01

    An apparatus has been developed for measuring time-dependent x-ray diffraction. X-ray pulses from an Advanced Light Source bend magnet are diffracted by a sagittally-focusing Si (111) crystal and then by a sample crystal, presently InSb (111). Laser pulses with 100 fs duration and a repetition rate of 1 KHz irradiate the sample inducing a phase transition. Two types of detectors are being employed: an x-ray streak camera and an avalanche photodiode. The streak camera is driven by a photoconductive switch and has a 2 ps temporal resolution determined by trigger jitter. The avalanche photodiode has high quantum efficiency and sufficient time resolution to detect single x-ray pulses in ALS two bunch or `camshaft' operation. A beamline is under construction dedicated for time resolved and micro-diffraction experiments. In the new beamline a toroidal mirror collects 3 mrad horizontally and makes a 1:1 image of the bend magnet source in the x-ray hutch. A laser induced phase transition has been observed in InSb occurring within 70 ps.

  9. Purification, crystallization and preliminary X-ray crystallographic analysis of rice Bowman–Birk inhibitor from Oryza sativa

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Yi-Hung [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Li, Hsin-Tai [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsinchu 30013,Taiwan (China); Huang, Yen-Chieh [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Hsieh, Ying-Cheng; Guan, Hong-Hsiang [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsinchu 30013,Taiwan (China); Liu, Ming-Yih [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Chang, Tschining; Wang, Andrew H.-J., E-mail: ahjwang@gate.sinica.edu.tw [Institute of Biological Chemistry, Academia Sinica, Taipei 11529,Taiwan (China); Chen, Chun-Jung, E-mail: ahjwang@gate.sinica.edu.tw [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Department of Physics, National Tsing-Hua University, Hsinchu 30013,Taiwan (China)

    2006-06-01

    Rice Bowman–Birk inhibitor was expressed and crystallized. Bowman–Birk inhibitors (BBIs) are cysteine-rich proteins with inhibitory activity against proteases that are widely distributed in monocot and dicot species. The expression of rice BBI from Oryza sativa is up-regulated and induced by pathogens or insects during germination of rice seeds. The rice BBI (RBTI) of molecular weight 15 kDa has been crystallized using the hanging-drop vapour-diffusion method. According to the diffraction of rice BBI crystals at a resolution of 2.07 Å, the unit cell belongs to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 74.37, b = 96.69, c = 100.36 Å. Preliminary analysis indicates four BBI molecules in an asymmetric unit, with a solvent content of 58.29%.

  10. Crystallization and preliminary X-ray diffraction analysis of an anti-H(O) lectin from Lotus tetragonolobus seeds.

    Science.gov (United States)

    Moreno, Frederico Bruno Mendes Batista; Martil, Daiana Evelin; Cavada, Benildo Sousa; de Azevedo, Walter Filgueira

    2006-07-01

    The seed lectin from Lotus tetragonolobus (LTA) has been crystallized. The best crystals grew over several days and were obtained using the vapour-diffusion method at a constant temperature of 293 K. A complete structural data set was collected at 2.00 angstroms resolution using a synchrotron-radiation source. LTA crystals were found to be monoclinic, belonging to space group P2(1), with unit-cell parameters a = 68.89, b = 65.83, c = 102.53 angstroms, alpha = gamma = 90, beta = 92 degrees. Molecular replacement yielded a solution with a correlation coefficient and R factor of 34.4 and 51.6%, respectively. Preliminary analysis of the molecular-replacement solution indicates a new quaternary association in the LTA structure. Crystallographic refinement is under way.

  11. Crystallization and preliminary X-ray diffraction analysis of an anti-H(O) lectin from Lotus tetragonolobus seeds

    Energy Technology Data Exchange (ETDEWEB)

    Moreno, Frederico Bruno Mendes Batista; Martil, Daiana Evelin [Programa de Pós-graduação em Biofísica Molecular, Departamento de Física, UNESP, São José do Rio Preto, SP 15054-000 (Brazil); Cavada, Benildo Sousa [BioMol-Lab UFC, Caixa Postal 6043, 60.455-970, Fortaleza-CE (Brazil); Azevedo, Walter Filgueira Jr de, E-mail: walter.junior@pucrs.br [Faculdade de Biociências-PUCRS, Av. Ipiranga 6681, Porto Alegre-RS, CEP 90619-900 (Brazil); Programa de Pós-graduação em Biofísica Molecular, Departamento de Física, UNESP, São José do Rio Preto, SP 15054-000 (Brazil)

    2006-07-01

    The seed lectin from Lotus tetragonolobus (LTA) has been crystallized. The best crystals grew over several days and were obtained using the vapour-diffusion method at a constant temperature of 293 K. The seed lectin from Lotus tetragonolobus (LTA) has been crystallized. The best crystals grew over several days and were obtained using the vapour-diffusion method at a constant temperature of 293 K. A complete structural data set was collected at 2.00 Å resolution using a synchrotron-radiation source. LTA crystals were found to be monoclinic, belonging to space group P2{sub 1}, with unit-cell parameters a = 68.89, b = 65.83, c = 102.53 Å, α = γ = 90, β = 92°. Molecular replacement yielded a solution with a correlation coefficient and R factor of 34.4 and 51.6%, respectively. Preliminary analysis of the molecular-replacement solution indicates a new quaternary association in the LTA structure. Crystallographic refinement is under way.

  12. X-ray wavefront modeling of Bragg diffraction from crystals

    Science.gov (United States)

    Sutter, John P.

    2011-09-01

    The diffraction of an X-ray wavefront from a slightly distorted crystal can be modeled by the Takagi-Taupin theory, an extension of the well-known dynamical diffraction theory for perfect crystals. Maxwell's equations applied to a perturbed periodic medium yield two coupled differential equations in the incident and diffracted amplitude. These equations are discretized for numerical calculation into the determination of the two amplitudes on the points of an integration mesh, beginning with the incident amplitudes at the crystal's top surface. The result is a set of diffracted amplitudes on the top surface (in the Bragg geometry) or the bottom surface (in the Laue geometry), forming a wavefront that in turn can be propagated through free space using the Fresnel- Huygens equations. The performance of the Diamond Light Source I20 dispersive spectrometer has here been simulated using this method. Methods are shown for transforming displacements calculated by finite element analysis into local lattice distortions, and for efficiently performing 3-D linear interpolations from these onto the Takagi-Taupin integration mesh, allowing this method to be extended to crystals under thermal load or novel mechanical bender designs.

  13. Crystal structure analysis of a hexatungstate by a high-energy X-ray diffraction experiment using an imaging plate Weissenberg camera at the BL04B2 beamline of SPring-8

    Energy Technology Data Exchange (ETDEWEB)

    Ozeki, Tomoji; Honma, Noritaka [Department of Chemistry and Materials Science, Tokyo Institute of Technology, Tokyo (Japan); Kusaka, Katsuhiro [Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Corporation (JST), Tokyo (Japan)

    2001-08-01

    An imaging plate Weissenberg camera was installed in the BL04B2 beamline of SPring-8 aiming at automated crystal structure determinations of small molecules. Since this beamline is designed to provide X-rays with the energies higher than 37 keV ({lambda}<0.33 A), this camera is advantageous in crystal structure analyses of heavily X-ray absorbing materials. The title crystal structure analysis led to precise positional parameters and well-behaved displacement parameters not only for heavy atoms but also for light atoms. (author)

  14. X-Ray Line Measurements with High Efficiency Bragg Crystals

    Energy Technology Data Exchange (ETDEWEB)

    Pak, A; Gregori, G; Knight, J; Campbell, K; Landen, O; Glenzer, S

    2004-04-01

    We have studied the focusing properties of two highly oriented pyrolitic graphite (HOPG) spectrometers, which differ in the degree of the mosaic spread: ZYA with a low mosaic spread ({gamma}=0.4 degrees) and ZYH with a large mosaic spread ({gamma}=3.5 degrees). In order to assess the crystal performance for a variety of different experiments, various K{alpha} and K{beta} x-ray lines have been produced using a high-intensity ({approx}>10{sup 17} W/cm{sup 2}) short-pulse ({approx} 100 fs) laser beam focused onto Ti, V, Zn, and Cu foils. The measured spectral resolution of the HOPG crystals in both first and second order diffraction has been compared with theoretical predictions. Using known values for the peak reflectivity of HOPG crystals, we have also computed K{alpha} x-ray conversion efficiencies of Ti, V, Zn, and Cu. These results are important to estimate the optimal conditions under which different types of HOPG monochromators can be used for the detection of weak x-ray signals as the one encountered in x-ray Thomson/Compton scattering experiments.

  15. Determination of organic crystal structures by X ray powder diffraction

    CERN Document Server

    McBride, L

    2000-01-01

    The crystal structure of Ibuprofen has been solved from synchrotron X-ray powder diffraction data using a genetic algorithm (GA). The performance of the GA is improved by incorporating prior chemical information in the form of hard limits on the values that can be taken by the flexible torsion angles within the molecule. Powder X-ray diffraction data were collected for the anti-convulsant compounds remacemide, remacemide nitrate and remacemide acetate at 130 K on BM 16 at the X-ray European Synchrotron Radiation Facility (ESRF) at Grenoble. High quality crystal structures were obtained using data collected to a resolution of typically 1.5 A. The structure determinations were performed using a simulated annealing (SA) method and constrained Rietveld refinements for the structures converged to chi sup 2 values of 1.64, 1.84 and 1.76 for the free base, nitrate and acetate respectively. The previously unknown crystal structure of the drug famotidine Form B has been solved using X-ray powder diffraction data colle...

  16. Purification, crystallization and preliminary X-ray crystallographic analysis of the CIDE-N domain of Fsp27.

    Science.gov (United States)

    Wang, Xiaodan; Zhang, Bo; Xu, Duo; Gao, Jinlan; Wang, Linfang; Wang, Zhi; Shan, Yaming; Yu, Xianghui

    2012-12-01

    Fsp27, a member of the CIDE protein family which is selectively expressed in adipocytes, has emerged as a novel regulator for unilocular lipid droplet (LD) formation, lipid metabolism, differentiation of adipocytes and insulin sensitivity. An LD is a subcellular compartment that is used by adipocytes for the efficient storage of fats. The CIDE-N domain of Fsp27 functions as a recruitment platform that induces the correct configuration of the Fsp27 CIDE-C domain to facilitate LD fusion. This study reports the high-yield expression of the mouse Fsp27 CIDE-N domain in Escherichia coli; a two-step purification protocol with high efficiency was established and crystallographic analysis was performed. The purity of the recombinant Fsp27 was >95% as assessed by SDS-PAGE. Crystals were obtained at 291 K using 28% polyethylene glycol 4000 as a precipitant. Diffraction data were collected to 1.92 Å resolution and the crystal belonged to space group P6(5), with unit-cell parameters a=b=63.3, c=37.4 Å, α=β=90, γ=120°. The components of the crystal were identified by ion-trap LC/MS/MS spectrometric analysis. The structure has been solved by molecular replacement and refinement is in progress.

  17. Crystallization and Preliminary X-ray analysis of Human Recombinant Acid beta-glucocerebrosidase, a treatment for Gaucher's Disease

    Science.gov (United States)

    Roeber, Dana F.; Achari, Aniruddha; Manavalan, Partha; Edmunds, Tim; Scott, David L.; Curreri, Peter A. (Technical Monitor)

    2002-01-01

    Acid beta-glucocerebrosidase (N-acylsphingosyl - O - beta-D - glucoside:glucohydrolase) is a lysosomal glycoprotein that catalyzes the hydrolysis of the glycolipid glucocerebroside to glucose and ceramide. Inadequate levels of this enzyme underly the pathophysiology of Gaucher's disease. Cerezyme(R) (Genzyme Corporation, Cambridge, MA) is a partially deglycosylated form of recombinant human acid beta-glucocerebrosidase that is commercially available for the treatment of Gaucher patients. Although acid beta-glucocerebrosidase belongs to a large family of glycosidases, relatively little is known regarding its structural biology. We report the crystallization and the initial diffraction analysis of Cerezyme(R). The crystals are C-centered orthorhombic, with unit-cell parameters of a = 285.0 A, b = 110.2 A, and c = 91.7 A. A 99.9 A complete data set has been collected to 2.75 A with an R(sub sym) of 8.8 %.

  18. Crystallization and preliminary X-ray analysis of recombinant human acid beta-glucocerebrosidase, a treatment for Gaucher's disease

    Science.gov (United States)

    Roeber, Dana; Achari, Aniruddha; Manavalan, Partha; Edmunds, Tim; Scott, David L.

    2003-01-01

    Acid beta-glucocerebrosidase (N-acylsphingosyl-1-O-beta-D-glucoside:glucohydrolase) is a lysosomal glycoprotein that catalyzes the hydrolysis of the glycolipid glucocerebroside to glucose and ceramide. Inadequate levels of this enzyme underly the pathophysiology of Gaucher's disease. Cerezyme (Genzyme Corporation, Cambridge, MA, USA) is a partially deglycosylated form of recombinant human acid beta-glucocerebrosidase that is used in the treatment of Gaucher patients. Although acid beta-glucocerebrosidase belongs to a large family of glycosidases, relatively little is known regarding its structural biology. Here, the crystallization and the initial diffraction analysis of Cerezyme are reported. The crystals are C-centered orthorhombic, with unit-cell parameters a = 285.0, b = 110.2, c = 91.7 A. A 99.9% complete data set has been collected to 2.75 A with an R(sym) of 8.8%.

  19. Crystallization and preliminary X-ray diffraction analysis of two extracytoplasmic solute receptors of the DctP family from Bordetella pertussis

    Energy Technology Data Exchange (ETDEWEB)

    Rucktooa, Prakash; Huvent, Isabelle [UMR8161 CNRS Institut de Biologie de Lille, Laboratoire de Cristallographie Macromoléculaire, 1 Rue du Professeur Calmette, BP 447, 59021 Lille CEDEX (France); IFR 142, Institut Pasteur de Lille, 1 Rue du Professeur Calmette, BP 245, 59021 Lille CEDEX (France); Antoine, Rudy; Lecher, Sophie; Jacob-Dubuisson, Françoise, E-mail: francoise.jacob@ibl.fr [IFR 142, Institut Pasteur de Lille, 1 Rue du Professeur Calmette, BP 245, 59021 Lille CEDEX (France); INSERM-U629, Lille (France); Institut Pasteur de Lille, 1 Rue du Professeur Calmette, BP 245, 59021 Lille CEDEX (France); Villeret, Vincent, E-mail: francoise.jacob@ibl.fr; Bompard, Coralie [UMR8161 CNRS Institut de Biologie de Lille, Laboratoire de Cristallographie Macromoléculaire, 1 Rue du Professeur Calmette, BP 447, 59021 Lille CEDEX (France); IFR 142, Institut Pasteur de Lille, 1 Rue du Professeur Calmette, BP 245, 59021 Lille CEDEX (France)

    2006-10-01

    Sample preparation, crystallization and preliminary X-ray analysis are reported for two B. pertussis extracytoplasmic solute receptors. DctP6 and DctP7 are two Bordetella pertussis proteins which belong to the extracytoplasmic solute receptors (ESR) superfamily. ESRs are involved in the transport of substrates from the periplasm to the cytosol of Gram-negative bacteria. DctP6 and DctP7 have been crystallized and diffraction data were collected using a synchrotron-radiation source. DctP6 crystallized in space group P4{sub 1}2{sub 1}2, with unit-cell parameters a = 108.39, b = 108.39, c = 63.09 Å, while selenomethionyl-derivatized DctP7 crystallized in space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 64.87, b = 149.83, c = 170.65 Å. The three-dimensional structure of DctP7 will be determined by single-wavelength anomalous diffraction, while the DctP6 structure will be solved by molecular-replacement methods.

  20. A versatile three/four crystal X-ray diffractometer for X-ray optical elements: Performance and applications

    DEFF Research Database (Denmark)

    Christensen, Finn Erland; Hornstrup, Allan; Jacobsen, E.;

    1987-01-01

    A versatile X-ray diffractometer for the study of X-ray optical elements such as grazing incidence mirrors, crystals and X-ray gratings has been built and put into operation at the Danish Space Research Institute. The diffractrometer is built on a 1.5 m long granite bench with the X-ray source...... located at one end of the bench where it can be rotated around a fixed vertical axis. The beam defining elements are perfect crystals of Si, Ge or quartz. With these it is possible to define a highly collimated beam of a few arcsec fwhm in the scattering plane. Examples of measurements on various X-ray...

  1. A putative siderophore-interacting protein from the marine bacterium Shewanella frigidimarina NCIMB 400: cloning, expression, purification, crystallization and X-ray diffraction analysis

    Energy Technology Data Exchange (ETDEWEB)

    Trindade, Inês B.; Fonseca, Bruno M. [Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157 Oeiras (Portugal); Matias, Pedro M. [Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157 Oeiras (Portugal); Instituto de Biologia Experimental e Tecnológica (iBET), Apartado 12, 2780-901 Oeiras (Portugal); Louro, Ricardo O.; Moe, Elin, E-mail: elinmoe@itqb.unl.pt [Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157 Oeiras (Portugal)

    2016-08-09

    The gene encoding a putative siderophore-interacting protein from the marine bacterium S. frigidimarina was successfully cloned, followed by expression and purification of the gene product. Optimized crystals diffracted to 1.35 Å resolution and preliminary crystallographic analysis is promising with respect to structure determination and increased insight into the poorly understood molecular mechanisms underlying iron acquisition. Siderophore-binding proteins (SIPs) perform a key role in iron acquisition in multiple organisms. In the genome of the marine bacterium Shewanella frigidimarina NCIMB 400, the gene tagged as SFRI-RS12295 encodes a protein from this family. Here, the cloning, expression, purification and crystallization of this protein are reported, together with its preliminary X-ray crystallographic analysis to 1.35 Å resolution. The SIP crystals belonged to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 48.04, b = 78.31, c = 67.71 Å, α = 90, β = 99.94, γ = 90°, and are predicted to contain two molecules per asymmetric unit. Structure determination by molecular replacement and the use of previously determined ∼2 Å resolution SIP structures with ∼30% sequence identity as templates are ongoing.

  2. Crystallization and preliminary X-ray analysis of RabX3, a tandem GTPase from Entamoeba histolytica.

    Science.gov (United States)

    Kumar Srivastava, Vijay; Chandra, Mintu; Datta, Sunando

    2014-07-01

    Ras superfamily GTPases regulate signalling pathways that control multiple biological processes by modulating the GTP/GDP cycle. Various Rab GTPases, which are the key regulators of vesicular trafficking pathways, play a vital role in the survival and virulence of the enteric parasite Entamoeba histolytica. The Rab GTPases act as binary molecular switches that utilize the conformational changes associated with the GTP/GDP cycle to elicit responses from target proteins and thereby regulate a broad spectrum of cellular processes including cell proliferation, cytoskeletal assembly, nuclear transport and intracellular membrane trafficking in eukaryotes. Entamoeba histolytica RabX3 (EhRabX3) is a unique GTPase in the amoebic genome, the only member in the eukaryotic Ras superfamily that harbours tandem G-domains and shares only 8-16% sequence identity with other GTPases. Recent studies suggested that EhRabX3 binds to a single guanine nucleotide through its N-terminal G-domain (NTD), while the C-terminal G-domain (CTD) plays a potential role in binding of the nucleotide to the NTD. Thus, understanding the intermolecular regulation between the two GTPase domains is expected to reveal valuable information on the overall action of EhRabX3. To provide structural insights into the inclusive action of this unique GTPase, EhRabX3 was crystallized by successive micro-seeding using the vapour-diffusion method. A complete data set was collected to 3.3 Å resolution using a single native EhRabX3 crystal at 100 K on BM14 at the ESRF, Grenoble, France. The crystal belonged to monoclinic space group C2, with unit-cell parameters a=198.6, b=119.3, c=89.2 Å, β=103.1°. Preliminary analysis of the data using the Matthews Probability Calculator suggested the presence of four to six molecules in the asymmetric unit.

  3. Solid state parameters, structure elucidation, High Resolution X-Ray Diffraction (HRXRD), phase matching, thermal and impedance analysis on L-Proline trichloroacetate (L-PTCA) NLO single crystals.

    Science.gov (United States)

    Kalaiselvi, P; Raj, S Alfred Cecil; Jagannathan, K; Vijayan, N; Bhagavannarayana, G; Kalainathan, S

    2014-11-11

    Nonlinear optical single crystal of L-Proline trichloroacetate (L-PTCA) was successfully grown by Slow Evaporation Solution Technique (SEST). The grown crystals were subjected to single crystal X-ray diffraction analysis to confirm the structure. From the single crystal XRD data, solid state parameters were determined for the grown crystal. The crystalline perfection has been evaluated using high resolution X-ray diffractometer. The frequencies of various functional groups were identified from FTIR spectral analysis. The percentage of transmittance was obtained from UV Visible spectral analysis. TGA-DSC measurements indicate the thermal stability of the crystal. The dielectric constant, dielectric loss and ac conductivity were measured by the impedance analyzer. The DC conductivity was calculated by the cole-cole plot method.

  4. Crystallization and preliminary X-ray crystallographic analysis of yeast prion protein Ure2p with shortened N-terminal

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    An orthorhombic crystal form of a recombinant yeast prion protein with shortened N-terminal, 90Ure2p, has been obtained. Crystals were grown by the vapordiffusion technique against a mother liquor containing imidazole. Crystals belong to the primitive orthorhombic lattice with the cell parameters a = 54.5 ?, b = 74.7 ?, c = 131.0 ?. The crystals diffract to beyond 3.0 ? resolution at a synchrotron beamline.

  5. Expression, crystallization and preliminary X-ray crystallographic analysis of XometC, a cystathionine γ-lyase-like protein from Xanthomonas oryzae pv. oryzae

    Energy Technology Data Exchange (ETDEWEB)

    Ngo, Phuong-Thuy Ho; Kim, Jin-Kwang [Department of Advanced Technology Fusion, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701 (Korea, Republic of); Kim, Hyesoon [Major in Life Science, College of Natural Sciences, Sangmyung University, 7 Hongji-dong, Jongno-gu, Seoul 110-743 (Korea, Republic of); Jung, Junho [Department of Advanced Technology Fusion, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701 (Korea, Republic of); Ahn, Yeh-Jin [Major in Life Science, College of Natural Sciences, Sangmyung University, 7 Hongji-dong, Jongno-gu, Seoul 110-743 (Korea, Republic of); Kim, Jeong-Gu; Lee, Byoung-Moo [Microbial Genetics Division, National Institute of Agricultural Biotechnology (NIAB), Rural Development Administration (RDA), Suwon 441-707 (Korea, Republic of); Kang, Hee-Wan, E-mail: kanghw2@hknu.ac.kr [Graduate School of Biotechnology and Information, Hankyong National University, Ansung 456-749 (Korea, Republic of); Kang, Lin-Woo, E-mail: kanghw2@hknu.ac.kr [Department of Advanced Technology Fusion, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701 (Korea, Republic of)

    2008-08-01

    XometC, a cystathionine γ-lyase-like protein from X. oryzae pv. oryzae and an antibacterial drug-target protein against bacterial blight, was cloned, purified and crystallized. Preliminary X-ray crystallographic analysis of XometC crystals was carried out. Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight of rice (Oryza sativa L.), one of the most devastating diseases of rice in most rice-growing countries. XometC, a cystathionine γ-lyase (CGL) like protein that is an antibacterial drug-target protein against Xoo, was cloned, expressed, purified and crystallized. CGL catalyzes the second step in the reverse-transsulfuration pathway, which is essential for the metabolic interconversion of the sulfur-containing amino acids cysteine and methionine. Crystals of two different shapes, plate-shaped and pyramid-shaped, diffracted to 2.9 and 3.2 Å resolution and belonged to the primitive orthogonal space group P2{sub 1}2{sub 1}2{sub 1} and the tetragonal space group P4{sub 1} (or P4{sub 3}), with unit-cell parameters a = 73.0, b = 144.9, c = 152.3 Å and a = b = 78.2, c = 300.7 Å, respectively. For the P2{sub 1}2{sub 1}2{sub 1} crystals, three or four monomers exist in the asymmetric unit with a corresponding V{sub M} of 3.02 or 2.26 Å{sup 3} Da{sup −1} and a solvent content of 59.3 or 45.7%. For the P4{sub 1} (or P4{sub 3}) crystals, four or five monomers exist in the asymmetric unit with a corresponding V{sub M} of 2.59 or 2.09 Å{sup 3} Da{sup −1} and a solvent content of 52.5 or 40.6%.

  6. Crystallization and X-ray analysis of the extracellular adhesion domain of Helicobacter pylori adhesin A: the significance of the cation composition in the crystallization precipitant.

    Science.gov (United States)

    Guo, Ling; Zhang, Jinyong; Cui, Liwei; Liu, Dong; Ma, Bo; Wang, Shufeng; Li, Haibo; Wu, Yuzhang; Liu, Wei

    2017-04-01

    Adherence to host cells is a crucial step in the process of bacterial infection, which is usually mediated by a number of outer membrane proteins identified as adhesins. Helicobacter pylori adhesin A (HpaA) is a member of the adhesin family that mediates the adherence of Helicobacter pylori to gastric epithelial cells, and consequently assists the bacteria in becoming a life-long colonizer of the human stomach. In this study, two constructs were made for the production of truncated HpaA proteins comprising residues 31-260 and 53-260, respectively. The products of both constructs were crystallized, but only the protein from the shorter construct (residues 53-260) formed crystals that were capable of diffraction. In the subsequent optimization trials, crystals in different forms were unexpectedly obtained by using lithium sulfate and ammonium sulfate as the precipitant. An X-ray data set was collected to 1.95 Å resolution on beamline BL18U1 at SSRF using a crystal grown with 1.92 M lithium sulfate, which belonged to space group P65 with unit-cell parameters a = b = 95.42, c = 54.72 Å, γ = 120°, while another crystal grown with 1.9 M ammonium sulfate diffracted to 2.60 Å resolution and the collected data set was indexed in space group P21212, with unit-cell parameters a = 121.01, b = 190.56, c = 106.31 Å. The collection of diffraction data has established a solid basis for structure determination.

  7. Matching X-ray beam and detector properties to protein crystals of different perfection

    Energy Technology Data Exchange (ETDEWEB)

    Nave, Colin, E-mail: colin.nave@diamond.ac.uk [Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom)

    2014-03-18

    Expressions are given to match X-ray data collection facilities to the intrinsic diffraction properties of crystals with different degrees of perfection. An analysis is given of the effect of different beam and detector parameters on the sharpness of recorded diffraction features for macromolecular crystals of different quality. The crystal quality parameters include crystal strain, crystal or mosaic block size and mosaic block misorientation. Calculations are given for instrument parameters such as angular resolution of the detector, beam divergence and wavelength bandpass to be matched to the intrinsic diffraction properties from these crystals with the aim of obtaining the best possible data out of each crystal. Examples are given using typical crystal imperfections obtained from the literature for both room-temperature and cryo-cooled crystals. Possible implications for the choice of X-ray source, beamline design, detector specifications, instrument set-up and data processing are discussed, together with the limitations of the approach.

  8. Purification, crystallization and preliminary X-ray diffraction analysis of an oomycete-derived Nep1-­like protein

    Science.gov (United States)

    Luberacki, Borries; Weyand, Michael; Seitz, Ulrich; Koch, Wolfgang; Oecking, Claudia; Ottmann, Christian

    2008-01-01

    The elicitor protein Nep1-like protein from the plant pathogen Pythium aphanidermatum was purified and crystallized using the hanging-drop vapour-diffusion method. A native data set was collected to 1.35 Å resolution at 100 K using synchrotron radiation. Since selenomethionine-labelled protein did not crystallize under the original conditions, a second crystal form was identified that yielded crystals that diffracted to 2.1 Å resolution. A multiple-wavelength anomalous dispersion (MAD) experiment was performed at 100 K and all four selenium sites were identified, which allowed solution of the structure. PMID:19052381

  9. Purification, crystallization and preliminary X-ray diffraction analysis of an oomycete-derived Nep1-like protein.

    Science.gov (United States)

    Luberacki, Borries; Weyand, Michael; Seitz, Ulrich; Koch, Wolfgang; Oecking, Claudia; Ottmann, Christian

    2008-12-01

    The elicitor protein Nep1-like protein from the plant pathogen Pythium aphanidermatum was purified and crystallized using the hanging-drop vapour-diffusion method. A native data set was collected to 1.35 A resolution at 100 K using synchrotron radiation. Since selenomethionine-labelled protein did not crystallize under the original conditions, a second crystal form was identified that yielded crystals that diffracted to 2.1 A resolution. A multiple-wavelength anomalous dispersion (MAD) experiment was performed at 100 K and all four selenium sites were identified, which allowed solution of the structure.

  10. Crystallization and preliminary X-ray analysis of a family 19 glycosyl hydrolase from Carica papaya latex

    Energy Technology Data Exchange (ETDEWEB)

    Huet, Joëlle, E-mail: jhuet@ulb.ac.be [Laboratoire de Chimie Générale (CP 206/4), Institut de Pharmacie, Université Libre de Bruxelles (ULB), Campus de la Plaine, Boulevard du Triomphe, B-1050 Bruxelles (Belgium); Azarkan, Mohamed [Laboratoire de Chimie Générale (CP 609), Faculté de Médecine, Université Libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, B-1070 Bruxelles (Belgium); Looze, Yvan [Laboratoire de Chimie Générale (CP 206/4), Institut de Pharmacie, Université Libre de Bruxelles (ULB), Campus de la Plaine, Boulevard du Triomphe, B-1050 Bruxelles (Belgium); Villeret, Vincent [CNRS-UMR 8161, Institut de Biologie de Lille, Université de Lille 1-Université de Lille 2-Institut Pasteur de Lille, IFR142, 1 Rue du Professeur Calmette, F-59021 Lille (France); Wintjens, René, E-mail: jhuet@ulb.ac.be [Laboratoire de Chimie Générale (CP 206/4), Institut de Pharmacie, Université Libre de Bruxelles (ULB), Campus de la Plaine, Boulevard du Triomphe, B-1050 Bruxelles (Belgium)

    2008-05-01

    A chitinase isolated from the latex of the tropical species Carica papaya has been crystallized. The addition of N-acetyl-d-glucosamine to the crystallization solution has improved the diffraction quality resolution of the crystal to 1.8 Å resolution. A chitinase isolated from the latex of the tropical species Carica papaya has been purified to homogeneity and crystallized. This enzyme belongs to glycosyl hydrolase family 19 and exhibits exceptional resistance to proteolysis. The initially observed crystals, which diffracted to a resolution of 2.0 Å, were improved through modification of the crystallization protocol. Well ordered crystals were subsequently obtained using N-acetyl-d-glucosamine, the monomer resulting from the hydrolysis of chitin, as an additive to the crystallization solution. Here, the characterization of a chitinase crystal that belongs to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 69.08, b = 44.79, c = 76.73 Å, β = 95.33° and two molecules per asymmetric unit, is reported. Diffraction data were collected to a resolution of 1.8 Å. Structure refinement is currently in progress.

  11. Crystal defect studies using x-ray diffuse scattering

    Energy Technology Data Exchange (ETDEWEB)

    Larson, B.C.

    1980-01-01

    Microscopic lattice defects such as point (single atom) defects, dislocation loops, and solute precipitates are characterized by local electronic density changes at the defect sites and by distortions of the lattice structure surrounding the defects. The effect of these interruptions of the crystal lattice on the scattering of x-rays is considered in this paper, and examples are presented of the use of the diffuse scattering to study the defects. X-ray studies of self-interstitials in electron irradiated aluminum and copper are discussed in terms of the identification of the interstitial configuration. Methods for detecting the onset of point defect aggregation into dislocation loops are considered and new techniques for the determination of separate size distributions for vacancy loops and interstitial loops are presented. Direct comparisons of dislocation loop measurements by x-rays with existing electron microscopy studies of dislocation loops indicate agreement for larger size loops, but x-ray measurements report higher concentrations in the smaller loop range. Methods for distinguishing between loops and three-dimensional precipitates are discussed and possibilities for detailed studies considered. A comparison of dislocation loop size distributions obtained from integral diffuse scattering measurements with those from TEM show a discrepancy in the smaller sizes similar to that described above.

  12. Expression, purification, crystallization and preliminary X-ray diffraction analysis of α-11 giardin from Giardia lamblia

    Energy Technology Data Exchange (ETDEWEB)

    Pathuri, Puja; Nguyen, Emily Tam [Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697 (United States); Luecke, Hartmut, E-mail: hudel@uci.edu [Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697 (United States); Department of Physiology and Biophysics, University of California, Irvine, CA 92697 (United States); Department of Information and Computer Sciences, University of California, Irvine, CA 92697 (United States)

    2006-11-01

    α-11 giardin from the intestinal protozoan parasite, G. lamblia has been cloned, expressed, purified and crystallized under two different conditions and in two different space groups. Crystals from the first condition diffracted to 1.1 Å and belong to a primitive orthorhombic space group and crystals obtained in the second condition diffracted to 2.93 Å and belong to a primitive monoclinic space group. α-11 Giardin, a protein from the annexin superfamily, is a 35.0 kDa protein from the intestinal protozoan parasite Giardia lamblia which triggers a form of diarrhea called giardiasis. Here, the cloning, expression, purification and the crystallization of α-11 giardin under two different conditions and in two different space groups is reported. Crystals from the first condition diffracted to 1.1 Å and belong to a primitive orthorhombic space group, while crystals from the second condition, which included calcium in the crystallization solution, diffracted to 2.93 Å and belong to a primitive monoclinic space group. Determination of the detailed atomic structure of α-11 giardin will provide a better insight into its biological function and might establish whether this class of proteins is a potential drug target against giardiasis.

  13. High-resolution x-ray analysis with multilayer gratings

    CERN Document Server

    Jonnard, Philippe; André, Jean-Michel; 10.1002/xrs.1128

    2013-01-01

    Periodic multilayers are nowadays widely used to perform x-ray analysis in the soft x-ray range (photon energy lower than 1 keV). However, they do not permit to obtain high-resolution spectra like natural or synthetic crystals. Thus, multilayers cannot resolve interferences between close x-ray lines. It has been shown and demonstrated experimentally that patterning a grating profile within a multilayer structure leads to a diffractive optics with improved resolving power. We illustrate the use of a Mo/B4C multilayer grating in the Fe L and C K spectral ranges, around 700 eV and 280 eV respectively. First, in the Fe L range, the improved spectral resolution enables us to distinguish the Fe L\\alpha and L\\beta emissions (separated by 13 eV). In addition, using a sample made of a mix of LiF and an iron ore, we show that it is possible to easily resolve the F K and Fe L emissions. These examples demonstrate that an improved x-ray analysis can be obtained with multilayer gratings when there is the need to study sam...

  14. Crystallization and preliminary X-ray diffraction analysis of FKBP12 complexed with a new neurotrophic ligand

    Institute of Scientific and Technical Information of China (English)

    LI Pengyun; WANG Liwei; WU Beili; SHU Cuiling; NIE Aihua; SHEN Beifen; LI Song; RAO Zihe

    2003-01-01

    A novel neurotrophic ligand, (3R)-4-(p-toluenesulfonyl)-1,4-thiazane-3-carboxylic acid-L-phenylalanine ethyl ester, has been complexed with the FK506 binding protein of 12 kD (FKBP12) and crystallized using the hanging-drop vapor-diffusion method in 0.1 mol/L Hepes Na (pH6.5) solution containing 15%~27% PEG10000. Crystals belong to the P21 space group, with unit cell parameters of a=42.0, b=30.4, c=42.4A , β=110.7°. The crystals diffract to a 1.8A resolution limit.

  15. Crystallization and preliminary X-ray crystallographic analysis of latent isoform PPO4 mushroom (Agaricus bisporus) tyrosinase.

    Science.gov (United States)

    Mauracher, Stephan Gerhard; Molitor, Christian; Al-Oweini, Rami; Kortz, Ulrich; Rompel, Annette

    2014-02-01

    Tyrosinase exhibits catalytic activity for the ortho-hydroxylation of monophenols to diphenols as well as their subsequent oxidation to quinones. Owing to polymerization of these quinones, brown-coloured high-molecular-weight compounds called melanins are generated. The latent precursor form of polyphenol oxidase 4, one of the six tyrosinase isoforms from Agaricus bisporus, was purified to homogeneity and crystallized. The obtained crystals belonged to space group C121 (two molecules per asymmetric unit) and diffracted to 2.78 Å resolution. The protein only formed crystals under low-salt conditions using the 6-tungstotellurate(VI) salt Na6[TeW6O24] · 22H2O as a co-crystallization agent.

  16. Crystallization and preliminary X-ray diffraction analysis of the diterpene cyclooctatin synthase (CYC) from Streptomyces sp. LZ35

    Science.gov (United States)

    Zhang, Xiulei; Shang, Guijun; Gu, Lichuan; Shen, Yuemao

    2014-01-01

    Terpenoids are a large and highly diverse group of natural products, with the most chemically diverse pool of structures. Terpene synthase is the key enzyme in the process of terpenoid synthesis. In this paper, the first diterpene synthase (CYC) of bacterial origin was successfully crystallized. Native and SeMet-derivative crystals diffracted to 1.75 and 2.6 Å resolution, respectively. The native crystal belonged to space group P212121, with unit-cell parameters a = 59.10, b = 101.73, c = 108.93 Å, and contained two molecules per asymmetric unit. The SeMet-derivative crystal belonged to space group P21, with unit-cell parameters a = 58.64, b = 109.47, c = 58.73 Å, β = 119.35°, and had two molecules per asymmetric unit. PMID:24598929

  17. Crystallization and preliminary X-ray crystallographic analysis of latent isoform PPO4 mushroom (Agaricus bisporus) tyrosinase

    Energy Technology Data Exchange (ETDEWEB)

    Mauracher, Stephan Gerhard; Molitor, Christian [Universität Wien, Althanstrasse 14, 1090 Wien (Austria); Al-Oweini, Rami; Kortz, Ulrich [Jacobs University, PO Box 750 561, 28759 Bremen (Germany); Rompel, Annette, E-mail: annette.rompel@univie.ac.at [Universität Wien, Althanstrasse 14, 1090 Wien (Austria)

    2014-01-23

    Polyphenol oxidase 4 (PPO4) from the natural source A. bisporus was crystallized in its latent precursor form (pro-tyrosinase; Ser2–Thr565) using the 6-tungstotellurate(VI) salt Na{sub 6}[TeW{sub 6}O{sub 24}]·22H{sub 2}O as a crystallization additive. Tyrosinase exhibits catalytic activity for the ortho-hydroxylation of monophenols to diphenols as well as their subsequent oxidation to quinones. Owing to polymerization of these quinones, brown-coloured high-molecular-weight compounds called melanins are generated. The latent precursor form of polyphenol oxidase 4, one of the six tyrosinase isoforms from Agaricus bisporus, was purified to homogeneity and crystallized. The obtained crystals belonged to space group C121 (two molecules per asymmetric unit) and diffracted to 2.78 Å resolution. The protein only formed crystals under low-salt conditions using the 6-tungstotellurate(VI) salt Na{sub 6}[TeW{sub 6}O{sub 24}]·22H{sub 2}O as a co-crystallization agent.

  18. Crystallization and preliminary X-ray analysis of a protease inhibitor from the latex of Carica papaya

    Energy Technology Data Exchange (ETDEWEB)

    Azarkan, Mohamed [Université Libre de Bruxelles, Faculty of Medicine, Protein Chemistry Unit, Campus Erasme (CP 609), 808 Route de Lennik, B-1070 Brussels (Belgium); Garcia-Pino, Abel [Department of Molecular and Cellular Interactions, Vlaams Interuniversitair Instituut voor Biotechnologie and Laboratorium voor Ultrastructuur, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel (Belgium); Dibiani, Rachid [Université Libre de Bruxelles, Faculty of Medicine, Protein Chemistry Unit, Campus Erasme (CP 609), 808 Route de Lennik, B-1070 Brussels (Belgium); Wyns, Lode; Loris, Remy, E-mail: reloris@vub.ac.be [Department of Molecular and Cellular Interactions, Vlaams Interuniversitair Instituut voor Biotechnologie and Laboratorium voor Ultrastructuur, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel (Belgium); Baeyens-Volant, Danielle [Université Libre de Bruxelles, Faculty of Medicine, Protein Chemistry Unit, Campus Erasme (CP 609), 808 Route de Lennik, B-1070 Brussels (Belgium)

    2006-12-01

    The Kunitz-type trypsin/chymotrypsin inhibitor isolated from C. papaya latex has been crystallized using the hanging-drop vapour-diffusion method. Two different crystal forms are observed, diffracting to 2.6 and 1.7 Å. A Kunitz-type protease inhibitor purified from the latex of green papaya (Carica papaya) fruits was crystallized in the presence and absence of divalent metal ions. Crystal form I, which is devoid of divalent cations, diffracts to a resolution of 2.6 Å and belongs to space group P3{sub 1} or P3{sub 2}. This crystal form is a merohedral twin with two molecules in the asymmetric unit and unit-cell parameters a = b = 74.70, c = 78.97 Å. Crystal form II, which was grown in the presence of Co{sup 2+}, diffracts to a resolution of 1.7 Å and belongs to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 44.26, b = 81.99, c = 140.89 Å.

  19. Crystallization and X-ray diffraction analysis of a putative bacterial class I labdane-related diterpene synthase.

    Science.gov (United States)

    Serrano-Posada, Hugo; Centeno-Leija, Sara; Rojas-Trejo, Sonia; Stojanoff, Vivian; Rodríguez-Sanoja, Romina; Rudiño-Piñera, Enrique; Sánchez, Sergio

    2015-09-01

    Labdane-related diterpenoids are natural products with potential pharmaceutical applications that are rarely found in bacteria. Here, a putative class I labdane-related diterpene synthase (LrdC) identified by genome mining in a streptomycete was successfully crystallized using the microbatch method. Crystals of the LrdC enzyme were obtained in a holo form with its natural cofactor Mg(2+) (LrdC-Mg(2+)) and in complex with inorganic pyrophosphate (PPi) (LrdC-Mg(2+)-PPi). Crystals of native LrdC-Mg(2+) diffracted to 2.50 Å resolution and belonged to the trigonal space group P3221, with unit-cell parameters a = b = 107.1, c = 89.2 Å. Crystals of the LrdC-Mg(2+)-PPi complex grown in the same conditions as the native enzyme with PEG 8000 diffracted to 2.36 Å resolution and also belonged to the trigonal space group P3221. Crystals of the LrdC-Mg(2+)-PPi complex grown in a second crystallization condition with PEG 3350 diffracted to 2.57 Å resolution and belonged to the monoclinic space group P21, with unit-cell parameters a = 49.9, b = 104.1, c = 66.5 Å, β = 111.4°. The structure was determined by the single-wavelength anomalous dispersion (SAD) technique using the osmium signal from a potassium hexachloroosmate (IV) derivative.

  20. Purification, crystallization and preliminary X-ray diffraction analysis of inner membrane complex (IMC) subcompartment protein 1 (ISP1) from Toxoplasma gondii.

    Science.gov (United States)

    Tonkin, Michelle L; Brown, Shannon; Beck, Josh R; Bradley, Peter J; Boulanger, Martin J

    2012-07-01

    The protozoan parasites of the Apicomplexa phylum are devastating global pathogens. Their success is largely due to phylum-specific proteins found in specialized organelles and cellular structures. The inner membrane complex (IMC) is a unique apicomplexan structure that is essential for motility, invasion and replication. The IMC subcompartment proteins (ISP) have recently been identified in Toxoplasma gondii and shown to be critical for replication, although their specific mechanisms are unknown. Structural characterization of TgISP1 was pursued in order to identify the fold adopted by the ISPs and to generate detailed insight into how this family of proteins functions during replication. An N-terminally truncated form of TgISP1 was purified from Escherichia coli, crystallized and subjected to X-ray diffraction analysis. Two crystal forms of TgISP1 belonging to space groups P4(1)32 or P4(3)32 and P2(1)2(1)2(1) diffracted to 2.05 and 2.1 Å resolution, respectively.

  1. Crystallization and preliminary X-ray analysis of a Kunitz-type inhibitor, textilinin-1 from Pseudonaja textilis textilis

    Energy Technology Data Exchange (ETDEWEB)

    Millers, Emma-Karin I. [School of Molecular and Microbial Sciences, University of Queensland, Brisbane 4072, QLD (Australia); Masci, Paul P. [School of Medicine, Southern Division, University of Queensland, Princess Alexandra Hospital, Woolloongabba, Brisbane 4102, QLD (Australia); Lavin, Martin F. [The Queensland Cancer Fund Research Unit, The Queensland Institute of Medical Research, PO Box, Royal Brisbane Hospital, Herston, Brisbane 4029, QLD (Australia); Jersey, John de; Guddat, Luke W., E-mail: luke.guddat@uq.edu.au [School of Molecular and Microbial Sciences, University of Queensland, Brisbane 4072, QLD (Australia)

    2006-07-01

    Crystals of a canonical inhibitor of plasmin from Australian Brown snake venom has been obtained. In complex with trypsin these diffract to 2.0 Å resolution, while the free inhibitor diffracts to 1.63 Å. Textilinin-1 (Txln-1), a Kunitz-type serine protease inhibitor, is a 59-amino-acid polypeptide isolated from the venom of the Australian Common Brown snake Pseudonaja textilis textilis. This molecule has been suggested as an alternative to aprotinin, also a Kunitz-type serine protease inhibitor, for use as an anti-bleeding agent in surgical procedures. Txln-1 shares only 47% amino-acid identity to aprotinin; however, six cysteine residues in the two peptides are in conserved locations. It is therefore expected that the overall fold of these molecules is similar but that they have contrasting surface features. Here, the crystallization of recombinant textilinin-1 (rTxln-1) as the free molecule and in complex with bovine trypsin (229 amino acids) is reported. Two organic solvents, phenol and 1,4-butanediol, were used as additives to facilitate the crystallization of free rTxln-1. Crystals of the rTxln-1–bovine trypsin complex diffracted to 2.0 Å resolution, while crystals of free rTxln-1 diffracted to 1.63 Å resolution.

  2. Preparation, crystallization and preliminary X-ray analysis of the methionine synthase (MetE) from Streptococcus mutans

    Energy Technology Data Exchange (ETDEWEB)

    Fu, Tian-Min; Zhang, Xiao-Yan; Li, Lan-Fen; Liang, Yu-He, E-mail: liangyh@pku.edu.cn; Su, Xiao-Dong [National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing 100871 (China); Department of Biochemistry and Molecular Biology, College of Life Sciences, Peking University, Beijing 100871 (China)

    2006-10-01

    Methionine synthase (MetE) from S. mutans was expressed, purified and crystallized. Diffraction data have been collected to 2.2 Å resolution. The Streptococcus mutans metE gene encodes methionine synthase (MetE), which catalyzes the direct transfer of a methyl group from methyltetrahydrofolate to homocysteine in the last step of methionine synthesis. metE was cloned into pET28a and the gene product was expressed at high levels in the Escherichia coli strain BL21 (DE3). MetE was purified to homogeneity using Ni{sup 2+}-chelating chromatography followed by size-exclusion chromatography. Crystals of the protein were obtained by the hanging-drop vapour-diffusion method and diffracted to 2.2 Å resolution. The crystal belongs to space group P2{sub 1}, with unit-cell parameters a = 52.85, b = 99.48, c = 77.88 Å, β = 94.55°.

  3. Crystallization and preliminary X-ray analysis of beta-alanine synthase from the yeast Saccharomyces kluyveri

    DEFF Research Database (Denmark)

    Dobritzsch, D.; Gojkovic, Zoran; Andersen, Birgit

    2003-01-01

    In eukaryotes and some bacteria, the third step of reductive pyrimidine catabolism is catalyzed by beta-alanine synthase (EC 3.5.1.6). Crystals of the recombinant enzyme from the yeast Saccharomyces kluyveri were obtained using sodium citrate as a precipitant. The crystals belong to space group P2......(1) (unit-cell parameters a=117.2, b=77.1, c=225.5 Angstrom, beta=95.0degrees) and contain four homodimers per asymmetric unit. Data were collected to 2.7 Angstrom resolution. Introduction of heavy atoms into the crystal lattice induced a different set of unit-cell parameters (a=61.0, b=77.9, c=110.......1 Angstrom, beta=97.2degrees) in the same space group P2(1), with only one homodimer per asymmetric unit....

  4. Crystallization and preliminary X-ray diffraction analysis of levansucrase (LsdA) from Gluconacetobacter diazotrophicus SRT4.

    Science.gov (United States)

    Martínez-Fleites, Carlos; Tarbouriech, Nicolas; Ortiz-Lombardia, Miguel; Taylor, Edward; Rodríguez, Armando; Ramírez, Ricardo; Hernández, Lázaro; Davies, Gideon J

    2004-01-01

    The endophytic bacterium Gluconacetobacter diazotrophicus SRT4 secretes a constitutively expressed levansucrase (LsdA; EC 2.4.1.10), which converts sucrose to fructo-oligosaccharides and levan. Fully active LsdA was purified to high homogeneity by non-denaturing reversed-phase HPLC and was crystallized at room temperature by the hanging-drop vapour-diffusion method using ammonium sulfate and ethanol as precipitants. The crystals are extremely sensitive, but native data have been collected to 2.5 A under cryogenic conditions using synchrotron radiation. LsdA crystals belong to the orthorhombic space group P22(1)2(1) or P2(1)2(1)2, with unit-cell parameters a = 53.80, b = 119.39, c = 215.10 A.

  5. Crystallization and X-ray diffraction analysis of nylon hydrolase (NylC) from Arthrobacter sp. KI72.

    Science.gov (United States)

    Nagai, Keisuke; Yasuhira, Kengo; Tanaka, Yusuke; Kato, Dai-ichiro; Takeo, Masahiro; Higuchi, Yoshiki; Negoro, Seiji; Shibata, Naoki

    2013-10-01

    Nylon hydrolase (NylC) encoded by Arthrobacter plasmid pOAD2 (NylCp2) was expressed in Escherichia coli JM109 and purified by ammonium sulfate fractionation, anion-exchange column chromatography and gel-filtration chromatography. NylCp2 was crystallized by the sitting-drop vapour-diffusion method with ammonium sulfate as a precipitant in 0.1 M HEPES buffer pH 7.5 containing 0.2 M NaCl and 25% glycerol. Diffraction data were collected from the native crystal to a resolution of 1.60 Å. The obtained crystal was spindle shaped and belonged to the C-centred orthorhombic space group C2221, with unit-cell parameters a=70.84, b=144.90, c=129.05 Å. A rotation and translation search gave one clear solution containing two molecules per asymmetric unit.

  6. Crystallization and preliminary X-ray crystallographic analysis of the catalytic domain of membrane type 1 matrix metalloproteinase

    Science.gov (United States)

    Ogata, Hideaki; Decaneto, Elena; Grossman, Moran; Havenith, Martina; Sagi, Irit; Lubitz, Wolfgang; Knipp, Markus

    2014-01-01

    Membrane type 1 matrix metalloproteinase (MT1-MMP) belongs to the large family of zinc-dependent endopeptidases termed MMPs that are located in the extracellular matrix. MT1-MMP was crystallized at 277 K using the vapour-diffusion method with PEG as a precipitating agent. Data sets for MT1-MMP were collected to 2.24 Å resolution at 100 K. The crystals belonged to space group P43212, with unit-cell parameters a = 62.99, c = 122.60 Å. The crystal contained one molecule per asymmetric unit, with a Matthews coefficient (V M) of 2.90 Å3 Da−1; the solvent content is estimated to be 57.6%. PMID:24637763

  7. Crystallization and preliminary X-ray diffraction analysis of the peripheral light-harvesting complex LH2 from Marichromatium purpuratum.

    Science.gov (United States)

    Cranston, Laura J; Roszak, Aleksander W; Cogdell, Richard J

    2014-06-01

    LH2 from the purple photosynthetic bacterium Marichromatium (formerly known as Chromatium) purpuratum is an integral membrane pigment-protein complex that is involved in harvesting light energy and transferring it to the LH1-RC `core' complex. The purified LH2 complex was crystallized using the sitting-drop vapour-diffusion method at 294 K. The crystals diffracted to a resolution of 6 Å using synchrotron radiation and belonged to the tetragonal space group I4, with unit-cell parameters a=b=109.36, c=80.45 Å. The data appeared to be twinned, producing apparent diffraction symmetry I422. The tetragonal symmetry of the unit cell and diffraction for the crystals of the LH2 complex from this species reveal that this complex is an octamer.

  8. Crystallization and preliminary X-ray analysis of the HA3 component of Clostridium botulinum type C progenitor toxin

    Energy Technology Data Exchange (ETDEWEB)

    Nakamura, Toshio; Tonozuka, Takashi; Kotani, Mao; Obata, Kanae [Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509 (Japan); Oguma, Keiji [Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Okayama 700-8558 (Japan); Nishikawa, Atsushi, E-mail: nishikaw@cc.tuat.ac.jp [Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509 (Japan); CREST, Japan Science and Technology Agency (Japan)

    2007-12-01

    HA3, a 70 kDa haemagglutinating protein, is a precursor form of HA3a and HA3b, the subcomponents of Clostridium botulinum type C 16S progenitor toxin. In this report, recombinant HA3 protein was overexpressed in Escherichia coli, purified and crystallized. HA3, a 70 kDa haemagglutinating protein, is a precursor form of HA3a and HA3b, the subcomponents of Clostridium botulinum type C 16S progenitor toxin. In this report, recombinant HA3 protein was overexpressed in Escherichia coli, purified and crystallized. Diffraction data were collected to 2.6 Å resolution and the crystal belonged to the hexagonal space group P6{sub 3}. Matthews coefficient and self-rotation function calculations indicate that there is probably one molecule of HA3 in the asymmetric unit. A search for heavy-atom derivatives has been undertaken.

  9. Purification, crystallization and preliminary X-ray diffraction analysis of Cif, a virulence factor secreted by Pseudomonas aeruginosa.

    Science.gov (United States)

    Bahl, Christopher D; MacEachran, Daniel P; O'Toole, George A; Madden, Dean R

    2010-01-01

    The opportunistic pathogen Pseudomonas aeruginosa secretes a protein that triggers the accelerated degradation of the cystic fibrosis transmembrane conductance regulator (CFTR) in airway epithelial cells. This protein, which is known as the CFTR inhibitory factor (Cif), acts as a virulence factor and may facilitate airway colonization by P. aeruginosa. Based on sequence similarity Cif appears to be an epoxide hydrolase (EH), but it lacks several of the conserved features found in the active sites of canonical members of the EH family. Here, the crystallization of purified recombinant Cif by vapor diffusion is reported. The crystals formed in space group C2, with unit-cell parameters a = 167.4, b = 83.6, c = 88.3 A, beta = 100.6 degrees . The crystals diffracted to 2.39 A resolution on a rotating-anode source. Based on the calculated Matthews coefficient (2.2 A(3) Da(-1)), it appears that the asymmetric unit contains four molecules.

  10. Isolation, crystallization and preliminary X-ray diffraction analysis of L-amino-acid oxidase from Vipera ammodytes ammodytes venom.

    Science.gov (United States)

    Georgieva, Dessislava; Kardas, Anna; Buck, Friedrich; Perbandt, Markus; Betzel, Christian

    2008-10-01

    L-Amino-acid oxidase from the venom of Vipera ammodytes ammodytes, the most venomous snake in Europe, was isolated and crystallized using the sitting-drop vapour-diffusion method. The solution conditions under which the protein sample was monodisperse were optimized using dynamic light scattering prior to crystallization. The crystals belonged to space group C2, with unit-cell parameters a = 198.37, b = 96.38, c = 109.11 A, beta = 92.56 degrees . Initial diffraction data were collected to 2.6 A resolution. The calculated Matthews coefficient is approximately 2.6 A(3) Da(-1) assuming the presence of four molecules in the asymmetric unit.

  11. Purification, crystallization and preliminary X-ray crystallographic analysis of human ppGpp hydrolase, Mesh1

    Directory of Open Access Journals (Sweden)

    Dawei Sun

    2010-09-01

    Full Text Available Bacterial SpoT is a Mn2+-dependent pyrophosphohydrolase to hydrolyze guanosine 3’-diphosphate-5’-diphosphate to guanosine diphosphate and pyrophosphate. In this study, SpoT ortholog from Homo sapiens (hMesh1, was over-expressed in Escherichia coli, purified and crystallized using hanging-drop vapour-diffusion method with polyethylene glycol and sodium citrate. The native crystal of hMesh1 was diffracted to 2.1 Å using a synchrotron-radiation source and belonged to the monoclinic space group P21 with cell dimensions of a = 53.27 Å, b = 62.61 Å, c = 52.45 Å and β= 94.96˚. The crystal contains two molecules in the asymmetric unit, with a solvent content of 44% and a Matthews coefficient VM value of 2.18 Å3/Da.

  12. Crystallization and preliminary X-ray crystallographic analysis of the oxysterol-binding protein Osh3 from Saccharomyces cerevisiae.

    Science.gov (United States)

    Tong, Junsen; Yang, Huiseon; Ha, Subin; Lee, Youngjin; Eom, Soo Hyun; Im, Young Jun

    2012-12-01

    Oxysterol-binding protein (OSBP) related proteins (ORPs) are conserved from yeast to humans and are implicated in regulation of sterol homeostasis and in signal transduction pathways. Osh3 of Saccharomyces cerevisiae is a pleckstrin-homology (PH) domain-containing ORP member that regulates phosphoinositide metabolism at endoplasmic reticulum-plasma membrane contact sites. The N-terminal PH domain of Osh3 was purified and crystallized as a lysozyme fusion and the resulting crystal diffracted to 2.3 Å resolution. The crystal belonged to the monoclinic space group C2, with unit-cell parameters a=98.03, b=91.31, c=84.13 Å, β=81.41°. With two molecules in the asymmetric unit, the Matthews coefficient was 3.13 Å3 Da(-1). Initial attempts to solve the structure by molecular-replacement techniques using T4 lysozyme as a search model were successful. The C-terminal OSBP-related domain (OBD) of Osh3 was crystallized by the vapour-diffusion method and the resulting crystal diffracted to 1.5 Å resolution. The crystal was orthorhombic, belonging to space group P2(1)2(1)2(1), with unit-cell parameters a=41.57, b=87.52, c=100.58 Å. With one molecule in the asymmetric unit, the Matthews coefficient was 2.01 Å3 Da(-1). Initial attempts to solve the structure by the single-wavelength anomalous dispersion technique using bromine were successful.

  13. Purification, crystallization and preliminary X-ray diffraction analysis of the Fyn SH2 domain and its complex with a phosphotyrosine peptide.

    Science.gov (United States)

    Huculeci, Radu; Buts, Lieven; Lenaerts, Tom; van Nuland, Nico A J; Garcia-Pino, Abel

    2012-03-01

    SH2 domains are widespread protein-binding modules that recognize phosphotyrosines and play central roles in intracellular signalling pathways. The SH2 domain of the human protein tyrosine kinase Fyn has been expressed, purified and crystallized in the unbound state and in complex with a high-affinity phosphotyrosine peptide. X-ray data were collected to a resolution of 2.00 Å for the unbound form and 1.40 Å for the protein in complex with the phosphotyrosine peptide.

  14. Crystallization and preliminary X-ray crystallographic analysis of two vascular apoptosis-inducing proteins (VAPs) from Crotalus atrox venom

    Energy Technology Data Exchange (ETDEWEB)

    Igarashi, Tomoko; Oishi, Yuko [Department of Cardiac Physiology, National Cardiovascular Center Research Institute, 5-7-1 Fujishiro-dai, Suita, Osaka 565-8565 (Japan); Araki, Satohiko [Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Toba, Mie 517-0004 (Japan); Mori, Hidezo [Department of Cardiac Physiology, National Cardiovascular Center Research Institute, 5-7-1 Fujishiro-dai, Suita, Osaka 565-8565 (Japan); Takeda, Soichi, E-mail: stakeda@ri.ncvc.go.jp [Department of Cardiac Physiology, National Cardiovascular Center Research Institute, 5-7-1 Fujishiro-dai, Suita, Osaka 565-8565 (Japan); Laboratory for Structural Biochemistry, Riken Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki, Sayo, Hyogo 679-5148 (Japan)

    2006-07-01

    Vascular apoptosis-inducing protein 1 (VAP1) and VAP2 from C. atrox venom were crystallized in variety of different crystal forms. Diffraction data sets were obtained to 2.5 and 2.15 Å resolution for VAP1 and VAP2, respectively. VAPs are haemorrhagic snake-venom toxins belonging to the reprolysin family of zinc metalloproteinases. In vitro, VAPs induce apoptosis specifically in cultured vascular endothelial cells. VAPs have a modular structure that bears structural homology to mammalian ADAMs (a disintegrin and metalloproteinases). VAP1 is a homodimer with a MW of 110 kDa in which the monomers are connected by a single disulfide bridge. VAP2 is homologous to VAP1 and exists as a monomer with a MW of 55 kDa. In the current study, several crystal forms of VAP1 and VAP2 were obtained using the vapour-diffusion method and diffraction data sets were collected using SPring-8 beamlines. The best crystals of VAP1 and VAP2 generated data sets to 2.5 and 2.15 Å resolution, respectively.

  15. Crystallization and X-ray diffraction analysis of the CH domain of the cotton kinesin GhKCH2

    Energy Technology Data Exchange (ETDEWEB)

    Qin, Xinghua [China Agricultural University, No. 2 Yuanmingyuanxilu, Haidian District, Beijing 100094, People’s Republic of (China); The Fourth Military Medical University, No. 169 Changlexi Road, Xincheng District, Xi’an 710032, People’s Republic of (China); Chen, Ziwei; Li, Ping; Liu, Guoqin, E-mail: liu@cau.edu.cn [China Agricultural University, No. 2 Yuanmingyuanxilu, Haidian District, Beijing 100094, People’s Republic of (China)

    2016-02-19

    The cloning, expression, purification and crystallization of the CH domain of the plant-specific kinesin GhKCH2 is reported. GhKCH2 belongs to a group of plant-specific kinesins (KCHs) containing an actin-binding calponin homology (CH) domain in the N-terminus. Previous studies revealed that the GhKCH2 CH domain (GhKCH2-CH) had a higher affinity for F-actin (K{sub d} = 0.42 ± 0.02 µM) than most other CH-domain-containing proteins. To understand the underlying mechanism, prokaryotically expressed GhKCH2-CH (amino acids 30–166) was purified and crystallized. Crystals were grown by the sitting-drop vapour-diffusion method using 0.1 M Tris–HCl pH 7.0, 20%(w/v) PEG 8000 as a precipitant. The crystals diffracted to a resolution of 2.5 Å and belonged to space group P2{sub 1}, with unit-cell parameters a = 41.57, b = 81.92, c = 83.00 Å, α = 90.00, β = 97.31, γ = 90.00°. Four molecules were found in the asymmetric unit with a Matthews coefficient of 2.22 Å{sup 3} Da{sup −1}, corresponding to a solvent content of 44.8%.

  16. Crystallization and preliminary X-ray crystallographic analysis of polyphenol oxidase from Juglans regia (jrPPO1).

    Science.gov (United States)

    Zekiri, Florime; Bijelic, Aleksandar; Molitor, Christian; Rompel, Annette

    2014-06-01

    Tyrosinase is a type 3 copper enzyme that catalyzes the ortho-hydroxylation of monophenols to diphenols as well as their subsequent oxidation to quinones, which are precursors for the biosynthesis of melanins. The first plant tyrosinase from walnut leaves (Juglans regia) was purified to homogeneity and crystallized. During the purification, two forms of the enzyme differing only in their C-termini [jrPPO1(Asp101-Pro444) and jrPPO1(Asp101-Arg445)] were obtained. The most abundant form jrPPO1(Asp101-Arg445), as described in Zekiri et al. [Phytochemistry (2014), 101, 5-15], was crystallized, resulting in crystals that belonged to space group C121, with unit-cell parameters a=115.56, b=91.90, c=86.87 Å, α=90, β=130.186, γ=90°, and diffracted to 2.39 Å resolution. Crystals were only obtained from solutions containing at least 30% polyethylene glycol 5000 monomethyl ether in a close-to-neutral pH range.

  17. Crystallization and preliminary X-ray analysis of an enantioselective halohydrin dehalogenase from Agrobacterium radiobacter AD1

    NARCIS (Netherlands)

    Jong, René M. de; Rozeboom, Henriëtte J.; Kalk, Kor H.; Tang, Lixia; Janssen, Dick B.; Dijkstra, Bauke W.

    2002-01-01

    Halohydrin dehalogenases are key enzymes in the bacterial degradation of vicinal halopropanols and structurally related nematocides. Crystals of the enantioselective halohydrin dehalogenase HheC from Agrobacterium radiobacter AD1 have been obtained at room temperature from hanging-drop vapour-diffus

  18. Heterodimeric nitrate reductase (NapAB) from Cupriavidus necator H16: purification, crystallization and preliminary X-ray analysis

    Energy Technology Data Exchange (ETDEWEB)

    Coelho, Catarina; González, Pablo J.; Trincão, José; Carvalho, Ana L.; Najmudin, Shabir [REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica (Portugal); Hettman, Thomas; Dieckman, Stephan [Institute for Molecular Biotechnology, Beutenbergstrasse 11, 07745 Jena (Germany); Moura, José J. G.; Moura, Isabel; Romão, Maria J., E-mail: mromao@dq.fct.unl.pt [REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica (Portugal)

    2007-06-01

    Crystals of the oxidized form of the periplasmic nitrate reductase from Cupriavidus necator were obtained using polyethylene glycol 3350 as precipitant The periplasmic nitrate reductase from Cupriavidus necator (also known as Ralstonia eutropha) is a heterodimer that is able to reduce nitrate to nitrite. It comprises a 91 kDa catalytic subunit (NapA) and a 17 kDa subunit (NapB) that is involved in electron transfer. The larger subunit contains a molybdenum active site with a bis-molybdopterin guanine dinucleotide cofactor as well as one [4Fe–4S] cluster, while the small subunit is a di-haem c-type cytochrome. Crystals of the oxidized form of this enzyme were obtained using polyethylene glycol 3350 as precipitant. A single crystal grown at the High Throughput Crystallization Laboratory of the EMBL in Grenoble diffracted to beyond 1.5 Å at the ESRF (ID14-1), which is the highest resolution reported to date for a nitrate reductase. The unit-cell parameters are a = 142.2, b = 82.4, c = 96.8 Å, β = 100.7°, space group C2, and one heterodimer is present per asymmetric unit.

  19. Crystallization and X-ray diffraction analysis of salicylate synthase, a chorismate-utilizing enyme involved in siderophore biosynthesis

    Energy Technology Data Exchange (ETDEWEB)

    Parsons, James F., E-mail: parsonsj@umbi.umd.edu; Shi, Katherine; Calabrese, Kelly [Center for Advanced Research in Biotechnology, The University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850 (United States); Ladner, Jane E. [Center for Advanced Research in Biotechnology, The University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850 (United States); National Institute of Standards and Technology (United States)

    2006-03-01

    Salicylate synthase, which catalyzes the first step in the synthesis of the siderophore yersiniabactin, has been crystallized. Diffraction data have been collected to 2.5 Å. Bacteria have evolved elaborate schemes that help them thrive in environments where free iron is severely limited. Siderophores such as yersiniabactin are small iron-scavenging molecules that are deployed by bacteria during iron starvation. Several studies have linked siderophore production and virulence. Yersiniabactin, produced by several Enterobacteriaceae, is derived from the key metabolic intermediate chorismic acid via its conversion to salicylate by salicylate synthase. Crystals of salicylate synthase from the uropathogen Escherichia coli CFT073 have been grown by vapour diffusion using polyethylene glycol as the precipitant. The monoclinic (P2{sub 1}) crystals diffract to 2.5 Å. The unit-cell parameters are a = 57.27, b = 164.07, c = 59.04 Å, β = 108.8°. The solvent content of the crystals is 54% and there are two molecules of the 434-amino-acid protein in the asymmetric unit. It is anticipated that the structure will reveal key details about the reaction mechanism and the evolution of salicylate synthase.

  20. Crystallization and preliminary X-ray analysis of Thermoactinomyces vulgaris R-47 maltooligosaccharide-metabolizing enzyme homologous to glucoamylase

    OpenAIRE

    Ichikawa, Kazuhiro; Tonozuka, Takashi; Mizuno, Masahiro; Tanabe, Yoshihiro; Kamitori, Shigehiro; Nishikawa, Atsushi; Sakano, Yoshiyuki

    2005-01-01

    A maltooligosaccharide-metabolizing enzyme from T. vulgaris R-47 (TGA) homologous to glucoamylase degrades maltooligosaccharides more efficiently than starch, unlike fungal glucoamylases. TGA was crystallized and the state of the protein in solution was analyzed by gel-filtration chromatography.

  1. In situ analysis of electrocrystallization process of metal electrodeposition with confocal energy dispersive X-ray diffraction based on polycapillary X-ray optics

    Energy Technology Data Exchange (ETDEWEB)

    Li, Fangzuo; Liu, Zhiguo [The Key Laboratory of Beam Technology and Materials Modification of the Ministry of Education, Beijing Normal University, Beijing 100875 (China); College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875 (China); Beijing Radiation Center, Beijing 100875 (China); Sun, Tianxi, E-mail: stx@bnu.edu.cn [The Key Laboratory of Beam Technology and Materials Modification of the Ministry of Education, Beijing Normal University, Beijing 100875 (China); College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875 (China); Beijing Radiation Center, Beijing 100875 (China); Yang, Chaolin; Sun, Weiyuan; Sun, Xuepeng [The Key Laboratory of Beam Technology and Materials Modification of the Ministry of Education, Beijing Normal University, Beijing 100875 (China); College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875 (China); Beijing Radiation Center, Beijing 100875 (China); Ma, Yongzhong [Center for Disease Control and Prevention of Beijing, Beijing 100013 (China); Ding, Xunliang [The Key Laboratory of Beam Technology and Materials Modification of the Ministry of Education, Beijing Normal University, Beijing 100875 (China); College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875 (China); Beijing Radiation Center, Beijing 100875 (China)

    2015-06-11

    The confocal energy dispersive X-ray diffraction (EDXRD) based on a polycapillary focusing X-ray lens (PFXRL) in excitation channel and a polycapillary parallel X-ray lens (PPXRL) in detection channel was presented to study the electrocrystallization process of metal electrodeposition. The input focal spot of the PPXRL and the output focal spot of the PFXRL was adjusted in a confocal configuration, and only the X-rays from the volume overlapped by the two foci could be accordingly detected by the detector. The experimental results demonstrated the confocal EDXRD could be used to in situ real-time analysis of electrochemical crystal growth process.

  2. Purification, crystallization and preliminary X-ray diffraction analysis of the Escherichia coli common pilus chaperone EcpB

    Energy Technology Data Exchange (ETDEWEB)

    Garnett, James A.; Diallo, Mamou; Matthews, Steve J., E-mail: s.j.matthews@imperial.ac.uk [Imperial College London, South Kensington, London SW7 2AZ (United Kingdom)

    2015-05-20

    In Escherichia coli, the common pilus (Ecp) belongs to an alternative chaperone–usher pathway that plays a major role in both early biofilm formation and host-cell adhesion. Initial attempts at crystallizing the chaperone EcpB using natively purified protein from the bacterial periplasm were not successful; however, after the isolation of EcpB under denaturing conditions and subsequent refolding, crystals were obtained at pH 8.0 using the sitting-drop method of vapour diffusion. This is the first time that this refolding strategy has been used to purify CU chaperones. Pili are key cell-surface components that allow the attachment of bacteria to both biological and abiotic solid surfaces, whilst also mediating interactions between themselves. In Escherichia coli, the common pilus (Ecp) belongs to an alternative chaperone–usher (CU) pathway that plays a major role in both early biofilm formation and host-cell adhesion. The chaperone EcpB is involved in the biogenesis of the filament, which is composed of EcpA and EcpD. Initial attempts at crystallizing EcpB using natively purified protein from the bacterial periplasm were not successful; however, after the isolation of EcpB under denaturing conditions and subsequent refolding, crystals were obtained at pH 8.0 using the sitting-drop method of vapour diffusion. Diffraction data have been processed to 2.4 Å resolution. These crystals belonged to the trigonal space group P3{sub 1}21 or P3{sub 2}21, with unit-cell parameters a = b = 62.65, c = 121.14 Å and one monomer in the asymmetric unit. Molecular replacement was unsuccessful, but selenomethionine-substituted protein and heavy-atom derivatives are being prepared for phasing. The three-dimensional structure of EcpB will provide invaluable information on the subtle mechanistic differences in biogenesis between the alternative and classical CU pathways. Furthermore, this is the first time that this refolding strategy has been used to purify CU chaperones, and it

  3. Protein preparation, crystallization and preliminary X-ray crystallographic analysis of Smu.1475c from caries pathogen Streptococcus mutans.

    Science.gov (United States)

    Zhou, Yan-Feng; Mi, Wei; Li, Lanfen; Zhang, Xiaoyan; Liang, Yu-He; Su, Xiao-Dong; Wei, Shicheng

    2006-02-01

    The gene smu.1475c encodes a putative protein of 211 residues in Streptococcus mutans, a primary pathogen for human dental caries. In this work, smu.1475c was cloned into pET28a and expressed in good amount from the E. coli strain BL21 (DE3). Smu.1475c protein was purified to homogeneity in a two-step procedure of Ni2+ chelating and size exclusion chromatography. Crystals were obtained by hanging-drop vapor-diffusion method and diffracted to 2.7 angstroms resolution. The crystal belongs to orthorhombic space group P2(1)2(1)2(1) with cell dimension of a = 68.3 angstroms, b = 105.9 angstroms, c = 136.2 angstroms. The asymmetric unit is expected to contain four molecules with solvent content of 49.4%.

  4. Expression,purification,crystallization,and preliminary X-ray diffraction analysis of the human TLE1 Q domain

    Institute of Scientific and Technical Information of China (English)

    Su Wang; Jiamu Du; Hua Tang; Xinyu Ding; Manwu Zha; Zhifei Xu

    2011-01-01

    Human transducin-like enhancer of split 1(TLE1)plays crucial roles in a number of developmental processes and is involved in pathogenesis of malignancy tumors.The N-terminal glutamine-rich domain(Q domain)of TLEI mediates its tetramerization and interactions with different DNA-binding transcription factors to regulate Notch and Wnt signaling pathways.To better understand the molecular mechanism of TLEI's functions in these pathways,we cloned,purified,and crystallized the TLE1 Q domain(TLEI-Q).The crystals belong to space group C2221,with the complete diffraction data of the native and Se-Met TLEI-Q collected to 3.5 and 4.1 A resolutions,respectively.The phasing-solving and model building are in progress.

  5. Crystallization and preliminary X-ray diffraction analysis of protein 14 from Sulfolobus islandicus filamentous virus (SIFV)

    DEFF Research Database (Denmark)

    Goulet, Adeline; Spinelli, Silvia; Campanacci, Valérie

    2006-01-01

    -labelled protein using sitting drops of 100-300 nl. Crystals belong to space group P6(2)22 or P6(4)22, with unit-cell parameters a = b = 68.1, c = 132.4 A. Diffraction data were collected to a maximum acceptable resolution of 2.95 and 3.20 A for the SeMet-labelled and native protein, respectively....

  6. Purification, crystallization and preliminary X-ray diffraction analysis of the Escherichia coli common pilus chaperone EcpB.

    Science.gov (United States)

    Garnett, James A; Diallo, Mamou; Matthews, Steve J

    2015-06-01

    Pili are key cell-surface components that allow the attachment of bacteria to both biological and abiotic solid surfaces, whilst also mediating interactions between themselves. In Escherichia coli, the common pilus (Ecp) belongs to an alternative chaperone-usher (CU) pathway that plays a major role in both early biofilm formation and host-cell adhesion. The chaperone EcpB is involved in the biogenesis of the filament, which is composed of EcpA and EcpD. Initial attempts at crystallizing EcpB using natively purified protein from the bacterial periplasm were not successful; however, after the isolation of EcpB under denaturing conditions and subsequent refolding, crystals were obtained at pH 8.0 using the sitting-drop method of vapour diffusion. Diffraction data have been processed to 2.4 Å resolution. These crystals belonged to the trigonal space group P3(1)21 or P3(2)21, with unit-cell parameters a = b = 62.65, c = 121.14 Å and one monomer in the asymmetric unit. Molecular replacement was unsuccessful, but selenomethionine-substituted protein and heavy-atom derivatives are being prepared for phasing. The three-dimensional structure of EcpB will provide invaluable information on the subtle mechanistic differences in biogenesis between the alternative and classical CU pathways. Furthermore, this is the first time that this refolding strategy has been used to purify CU chaperones, and it could be implemented in similar systems where it has not been possible to obtain highly ordered crystals.

  7. A novel approach for structure analysis of two-dimensional membrane protein crystals using x-ray powder diffraction data

    CERN Document Server

    Dilanian, Ruben A; Varghese, Jose N; Wilkins, Steve W; Oka, Toshihiko; Yagi, Naoto; Quiney, Harry M; Nugent, Keith A

    2010-01-01

    The application of powder diffraction methods in two-dimensional crystallography is regarded as intractable because of the uncertainties associated with overlapping reflections. Here, we report an approach that resolves these ambiguities and provides reliable low-resolution phase information directly from powder diffraction data. We apply our method to the recovery of the structure of the bacteriorhodopsin (bR) molecule to a resolution of 7 angstroms using only powder diffraction data obtained from two-dimensional purple membrane (PM) crystals.

  8. Crystallization and preliminary X-ray analysis of enoyl-acyl carrier protein reductase (FabK) from Streptococcus pneumoniae

    Energy Technology Data Exchange (ETDEWEB)

    Saito, Jun, E-mail: jun-saito@meiji.co.jp; Yamada, Mototsugu; Watanabe, Takashi; Kitagawa, Hideo; Takeuchi, Yasuo [Pharmaceutical Research Center, Meiji Seika Kaisha Ltd, 760 Morooka-cho, Kohoku-ku, Yokohama 222-8567 (Japan)

    2006-06-01

    Enoyl-acyl carrier protein (ACP) reductases are responsible for bacterial type II fatty-acid biosynthesis and are attractive targets for developing novel antibiotics. The S. pneumoniae enoyl-ACP reductase (FabK) was crystallized and selenomethionine MAD data were collected to 2 Å resolution. The enoyl-acyl carrier protein (ACP) reductase from Streptococcus pneumoniae (FabK; EC 1.3.1.9) is responsible for catalyzing the final step in each elongation cycle of fatty-acid biosynthesis. Selenomethionine-substituted FabK was purified and crystallized by the hanging-drop vapour-diffusion method at 277 K. The crystal belongs to space group P2{sub 1}, with unit-cell parameters a = 50.26, b = 126.70, c = 53.63 Å, β = 112.46°. Diffraction data were collected to 2.00 Å resolution using synchrotron beamline BL32B2 at SPring-8. Two molecules were estimated to be present in the asymmetric unit, with a solvent content of 45.1%.

  9. Purification, crystallization and preliminary X-ray diffraction analysis of saxthrombin, a thrombin-like enzyme from Gloydius saxatilis venom

    Energy Technology Data Exchange (ETDEWEB)

    Wei, Wenqing; Zhao, Wei [Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027 (China); Key Laboratory of Structural Biology, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui 230027 (China); Wang, Xiaoping [National Conservation of Snake Island and Laotieshan Mountain, Dalian, Liaoning, 116041 (China); Teng, Maikun, E-mail: mkteng@ustc.edu.cn; Niu, Liwen, E-mail: mkteng@ustc.edu.cn [Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027 (China); Key Laboratory of Structural Biology, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui 230027 (China)

    2007-08-01

    The thrombin-like enzyme saxthrombin has been purified from G. saxatilis snake venom. Crystallization conditions were found and a data set was obtained to 1.43 Å. The snake-venom thrombin-like enzymes (SVTLEs) are a class of serine proteinases that show fibrinogen-clotting and esterolytic activities. Most TLEs convert fibrinogen to fibrin by releasing either fibrinopeptide A or fibrinopeptide B and cannot activate factor XIII. The enzymes hydrolyze fibrinogen to produce non-cross-linked fibrins, which are susceptible to the lytic action of plasmin. Because of these physiological properties, TLEs have important medical applications in myocardial infarction, ischaemic stroke and thrombotic diseases. Here, a three-step chromatography procedure was used to purify saxthrombin (AAP20638) from Gloydius saxatilis venom to homogeneity. Its molecular weight is about 30 kDa as estimated by SDS–PAGE. A saxthrombin crystal was obtained using the hanging-drop vapour-diffusion method and diffracted to a resolution limit of 1.43 Å. The crystal belongs to space group C2, with unit-cell parameters a = 97.23, b = 52.21, c = 50.10 Å, β = 96.72°, and the Matthews coefficient (V{sub M}) was calculated to be 2.13 Å{sup 3} Da{sup −1} with one molecule in the asymmetric unit.

  10. Complex assembly, crystallization and preliminary X-ray crystallographic analysis of the human Rod-Zwilch-ZW10 (RZZ) complex.

    Science.gov (United States)

    Altenfeld, Anika; Wohlgemuth, Sabine; Wehenkel, Annemarie; Vetter, Ingrid R; Musacchio, Andrea

    2015-04-01

    The spindle-assembly checkpoint (SAC) monitors kinetochore-microtubule attachment during mitosis. In metazoans, the three-subunit Rod-Zwilch-ZW10 (RZZ) complex is a crucial SAC component that interacts with additional SAC-activating and SAC-silencing components, including the Mad1-Mad2 complex and cytoplasmic dynein. The RZZ complex contains two copies of each subunit and has a predicted molecular mass of ∼800 kDa. Given the low abundance of the RZZ complex in natural sources, its recombinant reconstitution was attempted by co-expression of its subunits in insect cells. The RZZ complex was purified to homogeneity and subjected to systematic crystallization attempts. Initial crystals containing the entire RZZ complex were obtained using the sitting-drop method and were subjected to optimization to improve the diffraction resolution limit. The crystals belonged to space group P3₁ (No. 144) or P3₂ (No. 145), with unit-cell parameters a = b = 215.45, c = 458.7 Å, α = β = 90.0, γ = 120.0°.

  11. Heterodimeric nitrate reductase (NapAB) from Cupriavidus necator H16: purification, crystallization and preliminary X-ray analysis

    Science.gov (United States)

    Coelho, Catarina; González, Pablo J.; Trincão, José; Carvalho, Ana L.; Najmudin, Shabir; Hettman, Thomas; Dieckman, Stephan; Moura, José J. G.; Moura, Isabel; Romão, Maria J.

    2007-01-01

    The periplasmic nitrate reductase from Cupriavidus necator (also known as Ralstonia eutropha) is a heterodimer that is able to reduce nitrate to nitrite. It comprises a 91 kDa catalytic subunit (NapA) and a 17 kDa subunit (NapB) that is involved in electron transfer. The larger subunit contains a molybdenum active site with a bis-molybdopterin guanine dinucleotide cofactor as well as one [4Fe–4S] cluster, while the small subunit is a di-haem c-type cytochrome. Crystals of the oxidized form of this enzyme were obtained using polyethylene glycol 3350 as precipitant. A single crystal grown at the High Throughput Crystallization Laboratory of the EMBL in Grenoble diffracted to beyond 1.5 Å at the ESRF (ID14-1), which is the highest resolution reported to date for a nitrate reductase. The unit-cell parameters are a = 142.2, b = 82.4, c = 96.8 Å, β = 100.7°, space group C2, and one heterodimer is present per asymmetric unit. PMID:17554176

  12. Crystallization and preliminary X-ray diffraction analysis of Val57 mutants of the amyloidogenic protein human cystatin C

    Energy Technology Data Exchange (ETDEWEB)

    Orlikowska, Marta; Jankowska, Elzbieta; Borek, Dominika; Otwinowski, Zbyszek; Skowron, Piotr; Szymanska, Aneta (Gdansk); (UTSMC)

    2012-03-15

    Human cystatin C (hCC) is a low-molecular-mass protein (120 amino-acid residues, 13 343 Da) found in all nucleated cells. Its main physiological role is regulation of the activity of cysteine proteases. Biologically active hCC is a monomeric protein, but all crystallization efforts have resulted in a dimeric domain-swapped structure. Recently, two monomeric structures were reported for cystatin C variants. In one of them stabilization was achieved by abolishing the possibility of domain swapping by the introduction of an additional disulfide bridge connecting the two protein domains (Cys47-Cys69). In the second structure, reported by this group, the monomeric hCC fold was preserved by stabilization of the conformationally constrained loop (L1) by a single-amino-acid substitution (V57N). To further assess the influence of changes in the sequence and properties of loop L1 on the dimerization propensity of cystatin C, two additional hCC mutants were obtained: one with a residue favoured in {beta}-turns (V57D) and another with proline (V57P), a residue that is known to be a structural element that can rigidify but also broaden turns. Here, the expression, purification and crystallization of V57D and V57P variants of recombinant human cystatin C are described. Crystals were grown by the vapour-diffusion method. Several diffraction data sets were collected using a synchrotron source at the Advanced Photon Source, Argonne National Laboratory, Chicago, USA.

  13. Crystallization and preliminary X-ray analysis of RsbS from Moorella thermoacetica at 2.5 A resolution.

    Science.gov (United States)

    Quin, Maureen; Newman, Joseph; Firbank, Susan; Lewis, Richard J; Marles-Wright, Jon

    2008-03-01

    The thermophilic bacterium Moorella thermoacetica possesses an rsb operon that is related to the genetic locus common to many Gram-positive bacteria that regulates the activity of the stress-responsive sigma factor sigma(B). One of the gene products of this operon is RsbS, a single STAS-domain protein that is a component of higher order assemblies in Bacillus subtilis known as 'stressosomes'. It is expected that similar complexes are found in M. thermoacetica, but in this instance regulating the biosynthesis of cyclic di-GMP, a ubiquitous secondary messenger. Selenomethionine-labelled MtRsbS protein was crystallized at room temperature using the hanging-drop vapour-diffusion method. Crystals belonging to space group P2(1)2(1)2(1), with unit-cell parameters a = 51.07, b = 60.52, c = 89.28 A, diffracted to 2.5 A resolution on beamline I04 of the Diamond Light Source. The selenium substructure was solved using SHELX and it is believed that this represents the first reported ab initio crystal structure to be solved using diffraction data collected at DLS.

  14. Purification, Crystallization and Preliminary X-ray Diffraction Analysis of Cif, a Virulence Factor Secreted by Pseudomonas aeruginosa

    Energy Technology Data Exchange (ETDEWEB)

    Bahl, C.; MacEachran, D; O& apos; Toole, G; Madden, D

    2010-01-01

    The opportunistic pathogen Pseudomonas aeruginosa secretes a protein that triggers the accelerated degradation of the cystic fibrosis transmembrane conductance regulator (CFTR) in airway epithelial cells. This protein, which is known as the CFTR inhibitory factor (Cif), acts as a virulence factor and may facilitate airway colonization by P. aeruginosa. Based on sequence similarity Cif appears to be an epoxide hydrolase (EH), but it lacks several of the conserved features found in the active sites of canonical members of the EH family. Here, the crystallization of purified recombinant Cif by vapor diffusion is reported. The crystals formed in space group C2, with unit-cell parameters a = 167.4, b = 83.6, c = 88.3 {angstrom}, {beta} = 100.6{sup o}. The crystals diffracted to 2.39 {angstrom} resolution on a rotating-anode source. Based on the calculated Matthews coefficient (2.2 {angstrom}{sup 3} Da{sup -1}), it appears that the asymmetric unit contains four molecules.

  15. Fundamentals of energy dispersive X-ray analysis

    CERN Document Server

    Russ, John C; Kiessling, R; Charles, J

    1984-01-01

    Fundamentals of Energy Dispersive X-ray Analysis provides an introduction to the fundamental principles of dispersive X-ray analysis. It presents descriptions, equations, and graphs to enable the users of these techniques to develop an intuitive and conceptual image of the physical processes involved in the generation and detection of X-rays. The book begins with a discussion of X-ray detection and measurement, which is accomplished by one of two types of X-ray spectrometer: energy dispersive or wavelength dispersive. The emphasis is on energy dispersive spectrometers, given their rather wid

  16. Crystallization and preliminary X-ray crystallographic analysis of human RGS10 complexed with Gαi3

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Hyung Ki; Rhee, Kyung Hee [Life Sciences Division, Korea Institute of Science and Technology, Seoul 130-650 (Korea, Republic of); School of Life Sciences and Biotechnology, Korea University, Seoul 136-701 (Korea, Republic of); Kim, Chan-Wha [School of Life Sciences and Biotechnology, Korea University, Seoul 136-701 (Korea, Republic of); Hwang, Kwang Yeon; Kim, Eunice EunKyeong, E-mail: eunice@kist.re.kr [Life Sciences Division, Korea Institute of Science and Technology, Seoul 130-650 (Korea, Republic of)

    2005-09-01

    Human RGS10 and Gαi3 have been overexpressed and purified. Their complex has been crystallized (space group P4{sub 3}2{sub 1}2 or P4{sub 1}2{sub 1}2, unit-cell parameters a = 99.88, b = 99.88, c = 144.59 Å, α = β = γ = 90°) and diffraction data have been collected to 2.5 Å resolution using synchrotron radiation. G-protein-coupled receptors, which are major targets for drug discovery, play a major role in diverse physiological processes by relating changes in the extracellular environment to intracellular functions via activation of heterotrimeric G-proteins. However, G-protein activity is also modulated by a family of proteins called regulators of G-protein signalling (RGS), which are classified into six subfamilies. RGS10 belongs to the subgroup D/R12 and is known to act specifically on activated forms of three Gα proteins (Gαi3, Gαz and Gαo but not Gαs). It is abundantly expressed in brain and immune tissues and has been implicated in the pathophysiology of schizophrenia. The RGS domain of RGS10 was cloned, purified, complexed with human Gαi3 and crystallized. The crystals containing both RGS and Gαi3 belong to space group P4{sub 3}2{sub 1}2 (or P4{sub 1}2{sub 1}2), with unit-cell parameters a = 99.88, b = 99.88, c = 144.59 Å, α = β = γ = 90°. A full set of diffraction data were collected to 2.5 Å resolution at 100 K using synchrotron radiation at Pohang beamline 4A.

  17. Expression, crystallization and preliminary X-ray crystallographic analysis of alanine racemase from Acinetobacter baumannii OXA-23.

    Science.gov (United States)

    Nguyen, Dinh-Duc; Ngo, Ho-Phuong-Thuy; Hong, Myoung-ki; Pham, Tan-Viet; Lee, Jung Hun; Lee, Jae Jin; Kwon, Dae Beom; Lee, Sang Hee; Kang, Lin-Woo

    2013-09-01

    Acinetobacter baumannii has received much attention owing to its exceptional ability to develop resistance to currently available antibiotics. Alanine racemase (ALR) catalyzes the racemization of L-alanine to D-alanine with pyridoxal 5'-phosphate (PLP) as a cofactor. The D-alanine product is an essential component of the bacterial cell wall and ALR is a potential target for the development of novel antibacterial drugs. The alr gene from A. baumannii was cloned and the protein (AbALR) was expressed, purified and crystallized. The AbALR crystal diffracted to 2.3 Å resolution and belonged to the primitive orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 55.1, b = 85.0, c = 167.7 Å. Two protomers were present in the asymmetric unit, with a corresponding V(M) value of 2.3 Å(3) Da(-1) and a solvent content of 47.5%.

  18. Analysis of the stabilization process of indomethacin crystals via π-π and CH-π interactions measured by Raman spectroscopy and X-ray diffraction

    Science.gov (United States)

    Hattori, Yusuke; Otsuka, Makoto

    2016-09-01

    In this study, formations of π-π and CH-π interactions in the crystallization of amorphous indomethacin (IMC) were investigated by simultaneous Raman spectroscopy and X-ray diffraction (XRD) measurements. The activation energy obtained from the change in the peak at 1616 cm-1 corresponded to the energy obtained from the XRD diffraction peak at 21.6°. We suggest that the stable IMC crystal forms by carboxyl-carboxyl interactions, which is followed by CH-π and π-π interactions supporting stabilization in the indole and chlorophenyl rings.

  19. Cloning, expression, purification and crystallization as well as X-ray fluorescence and preliminary X-ray diffraction analyses of human ADP-ribosylhydrolase 1.

    Science.gov (United States)

    Kernstock, Stefan; Koch-Nolte, Friedrich; Mueller-Dieckmann, Jochen; Weiss, Manfred S; Mueller-Dieckmann, Christoph

    2009-05-01

    Human ADP-ribosylhydrolase 1 (hARH1, ADPRH) cleaves the glycosidic bond of ADP-ribose attached to an Arg residue of a protein. hARH1 has been cloned, expressed heterologously in Escherichia coli, purified and crystallized in complex with K(+) and ADP. The orthorhombic crystals contained one monomer per asymmetric unit, exhibited a solvent content of 43% and diffracted X-rays to a resolution of 1.9 A. A prerequisite for obtaining well diffracting crystals was the performance of X-ray fluorescence analysis on poorly diffracting apo hARH1 crystals, which revealed the presence of trace amounts of K(+) in the crystal. Adding K-ADP to the crystallization cocktail then resulted in a crystal of different morphology and with dramatically improved diffraction properties.

  20. Purification, crystallization and preliminary X-ray analysis of TP0435 (Tp17) from the syphilis spirochete Treponema pallidum.

    Science.gov (United States)

    Brautigam, Chad A; Deka, Ranjit K; Norgard, Michael V

    2013-04-01

    Syphilis, caused by the bacterial spirochete Treponema pallidum, remains a prominent sexually transmitted infection worldwide. Despite sequencing of the genome of this obligate human pathogen 15 years ago, the functions of a large number of the gene products of T. pallidum are still unknown, particularly with respect to those of the organism's periplasmic lipoproteins. To better understand their functions, a structural biology approach has been pursued. To this end, the soluble portion of the T. pallidum TP0435 lipoprotein (also known as Tp17) was cloned, hyper-expressed in Escherichia coli and purified to apparent homogeneity. The protein crystals obtained from this preparation diffracted to 2.4 Å resolution and had the symmetry of space group R3. In the hexagonal setting, the unit-cell parameters were a = b = 85.7, c = 85.4 Å.

  1. Purification, crystallization and preliminary X-ray diffraction analysis of the Staphylococcus epidermidis extracellular serine protease Esp.

    Science.gov (United States)

    Vengadesan, Krishnan; Macon, Kevin; Sugumoto, Shinya; Mizunoe, Yoshimitsu; Iwase, Tadayuki; Narayana, Sthanam V L

    2013-01-01

    Esp, an extracellular serine protease from Staphylococcus epidermidis, has been shown to inhibit S. aureus biofilm formation and nasal colonization. The full-length 27 kDa pro-Esp was purified and digested with thermolysin to obtain mature Esp. The mature Esp containing 216 residues crystallized in space group P2(1), with unit-cell parameters a = 39.5, b = 61.2, c = 42.5 Å, β = 98.2° and one molecule in the asymmetric unit, with an estimated solvent content of 42%. A diffraction data set has been collected to 1.8 Å resolution on a rotating-anode home-source facility.

  2. Binding mode of CA074, a specific irreversible inhibitor, to bovine cathepsin B as determined by X-ray crystal analysis of the complex.

    Science.gov (United States)

    Yamamoto, A; Hara, T; Tomoo, K; Ishida, T; Fujii, T; Hata, Y; Murata, M; Kitamura, K

    1997-05-01

    The binding mode of CA074 [N-(L-3-trans-propylcarbamoyl-oxirane-2-carbonyl)-L-isoleucyl-L-pr oline], a specific irreversible inhibitor, to bovine spleen cathepsin B was elucidated by X-ray crystal structure analysis of the complex at 2.2 A resolution (conventional R=0.185). Inconsistently with our model used for the development of CA074, the L-isoleucyl-L-proline and propylcarbamoyl moieties are located at the S' and S subsites, respectively. This unexpected binding is primarily due to (i) similar extended chain conformations (due to the same S configurations) at the oxirane C2 and C3 atoms of CA074 and (ii) the just fit formation of double hydrogen bonds between the carboxyl oxygens of L-proline and the imidazole nitrogens of His-110 and His-111 residues (these residues are missing in papain, the tertiary structure of which was used for the design of CA074). The oxirane C3 atom possessing the P' substituent is covalently bound to the Cys-29 Sgamma atom (C3-Sgamma=1.79 A) and the S configuration is maintained. The present result will provide useful information for characterizing the substrate-specificity of cathepsin B.

  3. Developing small vacuum spark as an x-ray source for calibration of an x-ray focusing crystal spectrometer

    Energy Technology Data Exchange (ETDEWEB)

    Ghomeishi, Mostafa; Adikan, Faisal Rafiq Mahamd [Photonic Research Group, Department of Electrical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur (Malaysia); Karami, Mohammad [Department of Mechanical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur (Malaysia)

    2012-10-15

    A new technique of x-ray focusing crystal spectrometers' calibration is the desired result. For this purpose the spectrometer is designed to register radiated copper K{alpha} and K{beta} lines by using a flat {alpha}-quartz crystal. This experiment uses pre-breakdown x-ray emissions in low vacuum of about 2.5-3 mbar. At this pressure the pinch will not form so the plasma will not radiate. The anode material is copper and the capacity of the capacitor bank is 22.6 nF. This experiment designed and mounted a repetitive triggering system to save the operator time making hundreds of shots. This emission amount is good for calibration and geometrical adjustment of an optical crystal x-ray focusing spectrometer.

  4. Developing small vacuum spark as an x-ray source for calibration of an x-ray focusing crystal spectrometer.

    Science.gov (United States)

    Ghomeishi, Mostafa; Karami, Mohammad; Adikan, Faisal Rafiq Mahamd

    2012-10-01

    A new technique of x-ray focusing crystal spectrometers' calibration is the desired result. For this purpose the spectrometer is designed to register radiated copper Kα and Kβ lines by using a flat α-quartz crystal. This experiment uses pre-breakdown x-ray emissions in low vacuum of about 2.5-3 mbar. At this pressure the pinch will not form so the plasma will not radiate. The anode material is copper and the capacity of the capacitor bank is 22.6 nF. This experiment designed and mounted a repetitive triggering system to save the operator time making hundreds of shots. This emission amount is good for calibration and geometrical adjustment of an optical crystal x-ray focusing spectrometer.

  5. Synchrotron X-Ray Reciprocal Space Mapping, Topography and Diffraction Resolution Studies of Macromolecular Crystal Quality

    Science.gov (United States)

    Boggon, T. J.; Helliwell, J. R.; Judge, Russell A.; Siddons, D. P.; Snell, Edward H.; Stojanoff, V.

    2000-01-01

    A comprehensive study of microgravity and ground grown chicken egg white lysozyme crystals is presented using synchrotron X-ray reciprocal space mapping, topography techniques and diffraction resolution. Microgravity crystals displayed, on average, reduced intrinsic mosaicities but no differences in terms of stress over their earth grown counterparts. Topographic analysis revealed that in the microgravity case the majority of the crystal was contributing to the peak of the reflection at the appropriate Bragg angle. In the earth case at the diffraction peak only a small volume of the crystal contributed to the intensity. The techniques prove to be highly complementary with the reciprocal space mapping providing a quantitative measure of the crystal mosaicity and stress (or variation in lattice spacing) and topography providing a qualitative overall assessment of the crystal in terms of its X-ray diffraction properties. Structural data collection was also carried out both at the synchrotron and in the laboratory.

  6. Hybrid Powder - Single Crystal X-Ray Diffraction Instrument for Planetary Mineralogical Analysis of Unprepared Samples Project

    Data.gov (United States)

    National Aeronautics and Space Administration — We propose to develop a planetary exploration XRD/XRF instrument based on a hybrid diffraction approach that complements powder XRD analysis, similar to that of the...

  7. Crystallization and X-ray diffraction data of Thermus flavus 5S rRNA helices

    Science.gov (United States)

    Vallazza, Marco; Senge, Andrea; Lippmann, Corinna; Perbandt, Markus; Betzel, Christian; Bald, Rolf; Erdmann, Volker A.

    2001-11-01

    5S rRNA is an essential component of the large ribosomal subunit in prokaryotes and eukaryotes. Its unknown function in the ribosome will eventually be revealed in part by structural studies. To promote crystallization and enhance resolution in X-ray diffraction the molecule was subdivided into five domains A-E. Several RNA oligonucleotides were chemically produced by solid-phase phosphoramidite synthesis in order to construct the domains of the 5S rRNA. An improved RNA-MPD-screen was applied in crystallization which covers a complete 2D matrix for the components used. Crystallization analysis resulted in preferred combinations of pH, polyamine, monovalent and divalent cations for short RNA molecules. Six types of crystals corresponding to the domains B, C and E of Thermus flavus 5S rRNA could be obtained which were suitable for X-ray diffraction. Four RNA helices consist of seven base pairs and two of eight base pairs. As special features, they contain two adenines in a bulge position or G : U wobble base pairs assumed to be involved in RNA-protein recognition. With an increase in crystal size an increase in resolution by X-ray analysis was observed. X-ray diffraction data were collected to 1.5 Å resolution using synchrotron radiation and cryogenic cooling techniques.

  8. A pyrrolo-tetrathiafulvalene cage: Synthesis and X-ray crystal structure

    DEFF Research Database (Denmark)

    Nielsen, Kent A.; Jeppesen, Jan O.; Levillain, Eric

    2002-01-01

    A novel type of tetrathiafulvalene-cage 4 containing three monopyrrolo-tetrathiafulvalene units has been prepared employing a general and efficient synthetic approach. X-ray crystal structure analysis revealed that the cage is able to accommodate solvent molecules within a cavity in the solid state....

  9. Femtosecond X-ray diffraction from two-dimensional protein crystals

    Directory of Open Access Journals (Sweden)

    Matthias Frank

    2014-03-01

    Full Text Available X-ray diffraction patterns from two-dimensional (2-D protein crystals obtained using femtosecond X-ray pulses from an X-ray free-electron laser (XFEL are presented. To date, it has not been possible to acquire transmission X-ray diffraction patterns from individual 2-D protein crystals due to radiation damage. However, the intense and ultrafast pulses generated by an XFEL permit a new method of collecting diffraction data before the sample is destroyed. Utilizing a diffract-before-destroy approach at the Linac Coherent Light Source, Bragg diffraction was acquired to better than 8.5 Å resolution for two different 2-D protein crystal samples each less than 10 nm thick and maintained at room temperature. These proof-of-principle results show promise for structural analysis of both soluble and membrane proteins arranged as 2-D crystals without requiring cryogenic conditions or the formation of three-dimensional crystals.

  10. Diffraction imaging for in-situ characterization of double-crystal x-ray monochromators

    CERN Document Server

    Stoupin, Stanislav; Heald, Steve M; Brewe, Dale; Meron, Mati

    2015-01-01

    Imaging of the Bragg reflected x-ray beam is proposed and validated as an in-situ method for characterization of performance of double-crystal monochromators under the heat load of intense synchrotron radiation. A sequence of images is collected at different angular positions on the reflectivity curve of the second crystal and analyzed. The method provides rapid evaluation of the wavefront of the exit beam, which relates to local misorientation of the crystal planes along the beam footprint on the thermally distorted first crystal. The measured misorientation can be directly compared to results of finite element analysis. The imaging method offers an additional insight on the local intrinsic crystal quality over the footprint of the incident x-ray beam.

  11. Parametric X-ray radiation in crystals theory, experiments and applications

    CERN Document Server

    Baryshevsky, Vladimir G; Ulyanenkov, Alexander P

    2005-01-01

    This systematic and comprehensive monograph is devoted to parametric X-ray radiation (PXR). This radiation is generated by the motion of electrons inside a crystal, whereby the emitted photons are diffracted by the crystal and the radiation intensity critically depends on the parameters of the crystal structure. Nowadays PXR is the subject of numerous theoretical and experimental studies throughout the world. The first part of the book is a theoretical treatment of PXR, which includes a new approach to describe the radiation process in crystals. The second part is a survey of PXR experimental results and the possible applications of PXR as a tool for crystal structure analysis and a source of tunable X-ray radiation.

  12. X-ray crystal structure and small-angle X-ray scattering of sheep liver sorbitol dehydrogenase

    Energy Technology Data Exchange (ETDEWEB)

    Yennawar, Hemant [Pennsylvania State University, 8 Althouse Laboratory, University Park, PA 16802 (United States); Møller, Magda [Cornell High Energy Synchrotron Source, Ithaca, NY 14853 (United States); University of Copenhagen, DK-2100 Copenhagen (Denmark); Gillilan, Richard [Cornell High Energy Synchrotron Source, Ithaca, NY 14853 (United States); Yennawar, Neela, E-mail: nhy1@psu.edu [Pennsylvania State University, 8 Althouse Laboratory, University Park, PA 16802 (United States)

    2011-05-01

    The X-ray crystal structure and a small-angle X-ray scattering solution structure of sheep liver sorbitol dehydrogenase have been determined. The details of the interactions that enable the tetramer scaffold to be the functional biological unit have been analyzed. The X-ray crystal structure of sheep liver sorbitol dehydrogenase (slSDH) has been determined using the crystal structure of human sorbitol dehydrogenase (hSDH) as a molecular-replacement model. slSDH crystallized in space group I222 with one monomer in the asymmetric unit. A conserved tetramer that superposes well with that seen in hSDH (despite belonging to a different space group) and obeying the 222 crystal symmetry is seen in slSDH. An acetate molecule is bound in the active site, coordinating to the active-site zinc through a water molecule. Glycerol, a substrate of slSDH, also occupies the substrate-binding pocket together with the acetate designed by nature to fit large polyol substrates. The substrate-binding pocket is seen to be in close proximity to the tetramer interface, which explains the need for the structural integrity of the tetramer for enzyme activity. Small-angle X-ray scattering was also used to identify the quaternary structure of the tetramer of slSDH in solution.

  13. X-ray Crystallography Facility

    Science.gov (United States)

    2000-01-01

    Edward Snell, a National Research Council research fellow at NASA's Marshall Space Flight Center (MSFC), prepares a protein crystal for analysis by x-ray crystallography as part of NASA's structural biology program. The small, individual crystals are bombarded with x-rays to produce diffraction patterns, a map of the intensity of the x-rays as they reflect through the crystal.

  14. Purification, crystallization and preliminary X-ray diffraction analysis of RafE, a sugar-binding lipoprotein from Streptococcus pneumoniae

    Energy Technology Data Exchange (ETDEWEB)

    Paterson, Neil G., E-mail: neison@chem.gla.ac.uk; Riboldi-Tunnicliffe, Alan [Department of Chemistry and WestCHEM, Glasgow Biomedical Research Centre (GBRC), University of Glasgow, 120 University Place, Glasgow G12 8TA,Scotland (United Kingdom); Mitchell, Timothy J. [Division of Infection and Immunity (IBLS), Glasgow Biomedical Research Centre (GBRC), University of Glasgow, 120 University Place, Glasgow G12 8TA,Scotland (United Kingdom); Isaacs, Neil W. [Department of Chemistry and WestCHEM, Glasgow Biomedical Research Centre (GBRC), University of Glasgow, 120 University Place, Glasgow G12 8TA,Scotland (United Kingdom)

    2006-07-01

    The mature form of RafE has been expressed, purified and crystallized. X-ray diffraction data have been collected to 3.65 and 2.90 Å resolution from native and selenomethionine-derivative crystals, respectively. Streptococcus pneumoniae contains a large number of sugar-transport systems and the system responsible for raffinose uptake has recently been identified. The substrate-binding protein component of this system shares strong sequence homology with the multiple sugar metabolism substrate-binding protein MsmE from S. mutans and contains a lipoprotein-attachment site at cysteine residue 23. A truncated form (residues 24–419) of RafE from S. pneumoniae was cloned and overexpressed in Escherichia coli. Native and selenomethionine-labelled protein have been crystallized in the hexagonal space group P6{sub 1}22. Diffraction data have been successfully phased to 2.90 Å using Se SAD data and model building is in progress.

  15. Expression, purification, crystallization and preliminary X-ray analysis of an NAD-dependent glyceraldehyde-3-phosphate dehydrogenase from Helicobacter pylori

    Energy Technology Data Exchange (ETDEWEB)

    Elliott, Paul R.; Mohammad, Shabaz; Melrose, Helen J.; Moody, Peter C. E., E-mail: pcem1@leicester.ac.uk [Henry Wellcome Laboratories for Structural Biology, University of Leicester, Leicester LE1 9HN (United Kingdom)

    2008-08-01

    Glyceraldehyde-3-phosphate dehydrogenase B from H. pylori has been cloned, expressed, purified and crystallized in the presence of NAD. Crystals of GAPDHB diffracted to 2.8 Å resolution and belonged to space group P6{sub 5}22, with unit-cell parameters a = b = 166.1, c = 253.1 Å. Helicobacter pylori is a dangerous human pathogen that resides in the upper gastrointestinal tract. Little is known about its metabolism and with the onset of antibiotic resistance new treatments are required. In this study, the expression, purification, crystallization and preliminary X-ray diffraction of an NAD-dependent glyceraldehyde-3-phosphate dehydrogenase from H. pylori are reported.

  16. Cationic cobaltammine as anion receptor: Synthesis, characterization, single crystal X-ray structure and packing analysis of hexaamminecobalt(III) chloride ( R, R)-tartrate monohydrate

    Science.gov (United States)

    Bala, Ritu; Sharma, Raj Pal; Venugopalan, Paloth; Harrison, William T. A.

    2007-03-01

    In an effort to utilize the [Co(NH 3) 6] 3+ cation as a new anion receptor (binding agent) for dihydroxy dicarboxylate anion i.e., tartrate, orange single crystals of hexaamminecobalt(III) chloride ( R, R)-tartrate monohydrate, [Co(NH 3) 6]Cl(C 4H 4O 6)·H 2O, were obtained by reacting hexaamminecobalt(III) chloride with potassium-sodium tartrate tetrahydrate in a 1:1 molar ratio in hot water. The single crystal X-ray structure determination of [Co(NH 3) 6]Cl(C 4H 4O 6)·H 2O revealed that a distinctive network of hydrogen bonding interactions (N-H⋯O, N-H⋯Cl -, O-H⋯O) stabilize the crystal lattice. This is the first complex salt of hexaamminecobalt(III) with dihydroxy dicarboxylate anion i.e., tartrate.

  17. Crystallization and preliminary X-ray diffraction analysis of P30, the transmembrane domain of pertactin, an autotransporter from Bordetella pertussis

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Yanshi; Black, Isobel; Roszak, Aleksander W.; Isaacs, Neil W., E-mail: n.isaacs@chem.gla.ac.uk [Department of Chemistry and WestChem, Glasgow Biomedical Research Centre, University of Glasgow, 120 University Place, Glasgow G12 8TA,Scotland (United Kingdom)

    2007-07-01

    P30, the transmembrane C-terminal domain of pertactin from B. pertussis has been crystallized after refolding in vitro. Preliminary X-ray crystallographic data are reported. P30, the 32 kDa transmembrane C-terminal domain of pertactin from Bordetella pertussis, is supposed to form a β-barrel inserted into the outer membrane for the translocation of the passenger domain. P30 was cloned and expressed in inclusion bodies in Escherichia coli. After refolding and purification, the protein was crystallized using the sitting-drop vapour-diffusion method at 292 K. The crystals diffract to a resolution limit of 3.5 Å using synchrotron radiation and belong to the hexagonal space group P6{sub 1}22, with unit-cell parameters a = b = 123.27, c = 134.43 Å.

  18. Purification, crystallization and preliminary X-ray analysis of aminoglycoside-2′′-phosphotransferase-Ic [APH(2′′)-Ic] from Enterococcus gallinarum

    Energy Technology Data Exchange (ETDEWEB)

    Byrnes, Laura J. [Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, CA 94025 (United States); Badarau, Adriana; Vakulenko, Sergei B. [Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 (United States); Smith, Clyde A., E-mail: csmith@slac.stanford.edu [Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, CA 94025 (United States)

    2008-02-01

    APH(2′′)-Ic is an enzyme that is responsible for high-level gentamicin resistance in E. gallinarum isolates. Crystals of the wild-type enzyme and three mutants have been prepared and a complete X-ray diffraction data set was collected to 2.15 Å resolution from an F108L crystal. Bacterial resistance to aminoglycoside antibiotics is primarily the result of deactivation of the drugs. Three families of enzymes are responsible for this activity, with one such family being the aminoglycoside phosphotransferases (APHs). The gene encoding one of these enzymes, aminoglycoside-2′′-phosphotransferase-Ic [APH(2′′)-Ic] from Enterococcus gallinarum, has been cloned and the wild-type protein (comprising 308 amino-acid residues) and three mutants that showed elevated minimum inhibitory concentrations towards gentamicin (F108L, H258L and a double mutant F108L/H258L) were expressed in Escherichia coli and subsequently purified. All APH(2′′)-Ic variants were crystallized in the presence of 14–20%(w/v) PEG 4000, 0.25 M MgCl{sub 2}, 0.1 M Tris–HCl pH 8.5 and 1 mM Mg{sub 2}GTP. The crystals belong to the monoclinic space group C2, with one molecule in the asymmetric unit. The approximate unit-cell parameters are a = 82.4, b = 54.2, c = 77.0 Å, β = 108.8°. X-ray diffraction data were collected to approximately 2.15 Å resolution from an F108L crystal at beamline BL9-2 at SSRL, Stanford, California, USA.

  19. Remote X-Ray Diffraction and X-Ray Fluorescence Analysis on Planetary Surfaces

    Science.gov (United States)

    Blake, David F.; DeVincenzi, D. (Technical Monitor)

    1999-01-01

    The legacy of planetary X-ray Diffraction (XRD) and X-ray Fluorescence (XRF) began in 1960 when W. Parish proposed an XRD instrument for deployment on the moon. The instrument was built and flight qualified, but the Lunar XRD program was cancelled shortly before the first human landing in 1969. XRF chemical data have been collected in situ by surface landers on Mars (Viking 1 & 2, Pathfinder) and Venus (Venera 13 & 14). These highly successful experiments provide critical constraints on our current understanding of surface processes and planetary evolution. However, the mineralogy, which is more critical to planetary surface science than simple chemical analysis, will remain unknown or will at best be imprecisely constrained until X-ray diffraction (XRD) data are collected. Recent progress in X-ray detector technology allows the consideration of simultaneous XRD (mineralogic analysis) and high-precision XRF (elemental analysis) in systems miniaturized to the point where they can be mounted on fixed landers or small robotic rovers. There is a variety of potential targets for XRD/XRF equipped landers within the solar system, the most compelling of which are the poles of the moon, the southern highlands of Mars and Europa.

  20. X-ray diagnostics for TFTR

    Energy Technology Data Exchange (ETDEWEB)

    von Goeler, S.; Hill, K.W.; Bitter, M.

    1982-12-01

    A short description of the x-ray diagnostic preparation for the TFTR tokamak is given. The x-ray equipment consists of the limiter x-ray monitoring system, the soft x-ray pulse-height-analysis-system, the soft x-ray imaging system and the x-ray crystal spectrometer. Particular attention is given to the radiation protection of the x-ray systems from the neutron environment.

  1. Measurement of X-ray beam emittance using crystal optics at an X-ray undulator beamline

    CERN Document Server

    Kohmura, Y; Awaji, M; Tanaka, T; Hara, T; Goto, S; Ishikawa, T

    2000-01-01

    We present a method of using crystal optics to measure the emittance of the X-ray source. Two perfect crystals set in (++) configuration work as a high-resolution collimator. The phase-space diagram (i.e. beam cross-section and angular distribution) could be determined without any assumptions on the light source. When the measurement is done at short wavelength radiation from undulator, the electron beam emittance is larger than the diffraction limit of the X-rays. Therefore, the electron beam emittance could be estimated. The measurement was done with the hard X-rays of 18.5 and 55 keV from an undulator beamline, BL 47XU, of SPring-8. The horizontal emittance of the X-ray beam was estimated to be about 7.6 nmrad, close to the designed electron beam emittance of the storage ring (7 nmrad). Some portions of the instrumental functions, such as the scattering by filters and windows along the beamline and the slight bent of the crystal planes of the monochromator, could not be precisely evaluated, but an upper li...

  2. Science Letters:Preparation, crystallization and preliminary X-ray diffraction analysis of PH1948, predicted RNA methyltransferase from Pyrococcus horikoshii

    Institute of Scientific and Technical Information of China (English)

    GAO Yong-gui; YAO Min; TANAKA Isao

    2005-01-01

    RNA methyltransferase is responsible for transferring methyl and resulting in methylation on the bases or ribose ring of RNA, which existed widely but mostly remains an open question. A recombinant protein PH1948 predicting RNA methyltransferase from Pyrococcus horikoshii OT3 has been crystallized. The crystals of selenomethionyl PH1948 belong to space group C2, with unit-cell parameters a=207.0 (A),b=43.1 (A), c= 118.2 (A), β=92.1°, and diffract X-rays to 2.2(A) resolution. The VM value was determined to be 2.8(A)3/Da, indicating the presence of four protein molecules in the asymmetric unit.

  3. Expression, purification, crystallization and preliminary X-ray analysis of eCGP123, an extremely stable monomeric green fluorescent protein with reversible photoswitching properties.

    Science.gov (United States)

    Don Paul, Craig; Traore, Daouda A K; Byres, Emma; Rossjohn, Jamie; Devenish, Rodney J; Kiss, Csaba; Bradbury, Andrew; Wilce, Matthew C J; Prescott, Mark

    2011-10-01

    Enhanced consensus green protein variant 123 (eCGP123) is an extremely thermostable green fluorescent protein (GFP) that exhibits useful negative reversible photoswitching properties. eCGP123 was derived by the application of both a consensus engineering approach and a recursive evolutionary process. Diffraction-quality crystals of recombinant eCGP123 were obtained by the hanging-drop vapour-diffusion method using PEG 3350 as the precipitant. The eCGP123 crystal diffracted X-rays to 2.10 Å resolution. The data were indexed in space group P1, with unit-cell parameters a = 74.63, b = 75.38, c = 84.51 Å, α = 90.96, β = 89.92, γ = 104.03°. The Matthews coefficient (V(M) = 2.26 Å(3) Da(-1)) and a solvent content of 46% indicated that the asymmetric unit contained eight eCGP123 molecules.

  4. Recombinant expression, purification, crystallization and preliminary X-ray diffraction analysis of the C-terminal DUF490963–1138 domain of TamB from Escherichia coli

    Science.gov (United States)

    Josts, Inokentijs; Grinter, Rhys; Kelly, Sharon M.; Mosbahi, Khedidja; Roszak, Aleksander; Cogdell, Richard; Smith, Brian O.; Byron, Olwyn; Walker, Daniel

    2014-01-01

    TamB is a recently described inner membrane protein that, together with its partner protein TamA, is required for the efficient secretion of a subset of autotransporter proteins in Gram-negative bacteria. In this study, the C-terminal DUF490963–1138 domain of TamB was overexpressed in Escherichia coli K-12, purified and crystallized using the sitting-drop vapour-diffusion method. The crystals belonged to the primitive trigonal space group P3121, with unit-cell parameters a = b = 57.34, c = 220.74 Å, and diffracted to 2.1 Å resolution. Preliminary secondary-structure and X-ray diffraction analyses are reported. Two molecules are predicted to be present in the asymmetric unit. Experimental phasing using selenomethionine-labelled protein will be undertaken in the future. PMID:25195908

  5. Purification, crystallization and preliminary X-ray diffraction analysis of GatD, a glutamine amidotransferase-like protein from Staphylococcus aureus peptidoglycan.

    Science.gov (United States)

    Vieira, Diana; Figueiredo, Teresa A; Verma, Anil; Sobral, Rita G; Ludovice, Ana M; de Lencastre, Hermínia; Trincao, Jose

    2014-05-01

    Amidation of peptidoglycan is an essential feature in Staphylococcus aureus that is necessary for resistance to β-lactams and lysozyme. GatD, a 27 kDa type I glutamine amidotransferase-like protein, together with MurT ligase, catalyses the amidation reaction of the glutamic acid residues of the peptidoglycan of S. aureus. The native and the selenomethionine-derivative proteins were crystallized using the sitting-drop vapour-diffusion method with polyethylene glycol, sodium acetate and calcium acetate. The crystals obtained diffracted beyond 1.85 and 2.25 Å, respectively, and belonged to space group P212121. X-ray diffraction data sets were collected at Diamond Light Source (on beamlines I02 and I04) and were used to obtain initial phases.

  6. The Swift X-ray Telescope Cluster Survey III: X-ray spectral analysis

    CERN Document Server

    Tozzi, P; Tundo, E; Liu, T; Rosati, P; Borgani, S; Tagliaferri, G; Campana, S; Fugazza, D; D'Avanzo, P

    2014-01-01

    (Abridged) We present a spectral analysis of a new, flux-limited sample of 72 X-ray selected clusters of galaxies identified with the X-ray Telescope (XRT) on board the Swift satellite down to a flux limit of ~10-14 erg/s/cm2 (SWXCS, Tundo et al. 2012). We carry out a detailed X-ray spectral analysis with the twofold aim of measuring redshifts and characterizing the properties of the Intra-Cluster Medium (ICM). Optical counterparts and spectroscopic or photometric redshifts are obtained with a cross-correlation with NED. Additional photometric redshifts are computed with a dedicated follow-up program with the TNG and a cross-correlation with the SDSS. We also detect the iron emission lines in 35% of the sample, and hence obtain a robust measure of the X-ray redshift zX. We use zX whenever the optical redshift is not available. Finally, for all the sources with measured redshift, background-subtracted spectra are fitted with a mekal model. We perform extensive spectral simulations to derive an empirical formul...

  7. In situ 3D topographic and shape analysis by synchrotron radiation X-ray microtomography for crystal form identification in polymorphic mixtures

    Science.gov (United States)

    Yin, Xian-Zhen; Xiao, Ti-Qiao; Nangia, Ashwini; Yang, Shuo; Lu, Xiao-Long; Li, Hai-Yan; Shao, Qun; He, You; York, Peter; Zhang, Ji-Wen

    2016-04-01

    Polymorphism denotes the existence of more than one crystal structure of a substance, and great practical and theoretical interest for the chemical and pharmaceutical industries. In many cases, it is challenging to produce a pure crystal form and establish a sensitive detection method for the identification of crystal form in a mixture of polymorphs. In this study, an accurate and sensitive method based on synchrotron radiation X-ray computed microtomography (SR-μCT) was devised to identify the polymorphs of clopidogrel bisulphate (CLP). After 3D reconstruction, crystal particles were extracted and dozens of structural parameters were calculated. Whilst, the particle shapes of the two crystal forms were all irregular, the surface of CLP II was found to be rougher than CLP I. In order to classify the crystal form based on the quantitative morphological property of particles, Volume Bias Percentage based on Surface Smoothing (VBP) was defined and a new method based on VBP was successfully developed, with a total matching rate of 99.91% for 4544 particles and a lowest detectable limit of 1%. More important for the mixtures in solid pharmaceutical formulations, the interference of excipients can be avoided, a feature cannot achieved by other available analytical methods.

  8. Hard x-ray single crystal bi-mirror.

    Science.gov (United States)

    Lyubomirskiy, M; Snigireva, I; Kuznetsov, S; Yunkin, V; Snigirev, A

    2015-05-15

    We report a novel hard x-ray interferometer consisting of two parallel channels manufactured in a single Si crystal by means of microfabrication technology. The sidewall surfaces of the channels, similar to mirrors, scatter at very small incident angles, acting equivalently to narrow micrometer size slits as in the Young double-slit interferometer. Experimental tests of the interferometer were performed at the ESRF ID06 beamline in the energy range from 12 to 16 keV. The interference patterns at different grazing incidence angles were recorded in the near- and far-field. Evaluation of the influence of the channel surface roughness on the visibility of interference fringes was performed. The proposed interferometer design allows the arrangement of mirrors at different split distances.

  9. Project Title: Radiochemical Analysis by High Sensitivity Dual-Optic Micro X-ray Fluorescence

    Energy Technology Data Exchange (ETDEWEB)

    Havrilla, George J.; Gao, Ning

    2002-06-01

    A novel dual-optic micro X-ray fluorescence instrument will be developed to do radiochemical analysis of high-level radioactive wastes at DOE sites such as Savannah River Site and Hanford. This concept incorporates new X-ray optical elements such as monolithic polycapillaries and double bent crystals, which focus X-rays. The polycapillary optic can be used to focus X-rays emitted by the X-ray tube thereby increasing the X-ray flux on the sample over 1000 times. Polycapillaries will also be used to collect the X-rays from the excitation site and screen the radiation background from the radioactive species in the specimen. This dual-optic approach significantly reduces the background and increases the analyte signal thereby increasing the sensitivity of the analysis. A doubly bent crystal used as the focusing optic produces focused monochromatic X-ray excitation, which eliminates the bremsstrahlung background from the X-ray source. The coupling of the doubly bent crystal for monochromatic excitation with a polycapillary for signal collection can effectively eliminate the noise background and radiation background from the specimen. The integration of these X-ray optics increases the signal-to-noise and thereby increases the sensitivity of the analysis for low-level analytes. This work will address a key need for radiochemical analysis of high-level waste using a non-destructive, multi-element, and rapid method in a radiation environment. There is significant potential that this instrumentation could be capable of on-line analysis for process waste stream characterization at DOE sites.

  10. X-Ray Diffraction Analysis Program

    Science.gov (United States)

    Wiedemann, K. E.; Unnam, J.; Naidu, S. V. N.; Houska, C. R.

    1986-01-01

    SOPAD separates overlapping peaks and analyzes derivatives of X-ray diffraction data. SOPAD helps analyst get most information out of available diffraction data. SOPAD uses Marquardt-type nonlinear regression routine to refine initial estimates of individual peak positions, intensities, shapes, and half-widths.

  11. Crystallization and preliminary X-ray diffraction analysis of the Pax9 paired domain bound to a DC5 enhancer DNA element.

    Science.gov (United States)

    Narasimhan, Kamesh; Hilbig, Antonia; Udayasuryan, Barath; Jayabal, Sriram; Kolatkar, Prasanna R; Jauch, Ralf

    2014-10-01

    Pax genes belong to a family of metazoan transcription factors that are known to play a critical role in eye, ear, kidney and neural development. The mammalian Pax family of transcription factors is characterized by a ∼128-amino-acid DNA-binding paired domain that makes sequence-specific contacts with DNA. The diversity in Pax gene activities emerges from complex modes of interaction with enhancer regions and heterodimerization with multiple interaction partners. Based on in vitro optimal binding-site selection studies and enhancer identification assays, it has been suggested that Pax proteins may recognize and bind their target DNA elements with different binding modes/topologies, however this hypothesis has not yet been structurally explored. One of the most extensively studied DNA target elements of the Pax6 paired domain is the eye-lens specific DC5 (δ-crystallin) enhancer element. In order to shed light on Pax6-DC5 DNA interactions, the related paired-domain prototype Pax9 was crystallized with the minimal δ-crystallin DC5 enhancer element and preliminary X-ray diffraction analysis was attempted. A 3.0 Å resolution native data set was collected at the National Synchrotron Light Source (NSLS), Brookhaven from crystals grown in a solution consisting of 10%(w/v) PEG 20K, 20%(v/v) PEG 550 MME, 0.03 M NaNO3, 0.03 M Na2HPO4, 0.03 M NH2SO4, 0.1 M MES/imidazole pH 6.5. The data set was indexed and merged in space group C2221, with unit-cell parameters a = 75.74, b = 165.59, c = 70.14 Å, α = β = γ = 90°. The solvent content in the unit cell is consistent with the presence of one Pax9 paired domain bound to duplex DNA in the asymmetric unit.

  12. X-ray driven channeling acceleration in crystals and carbon nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Shin, Young-Min; Still, Dean A.; Shiltsev, Vladimir

    2013-12-01

    Acceleration of particles channeling in a crystal by means of diffracted x-rays via Bormann anomalous transmission was conceived for heavy ions and muons by Tajima and Cavenago [Phys. Rev. Lett. 59, 1440 (1987)], which potentially offers an appreciably high field gradient on the order of GV/cm. The theoretical model of the high gradient acceleration has been studied in two kinds of atomic structure, crystals and carbon nanotubes (CNTs), with analytic calculations and electromagnetic eigenmode simulations. A range of acceleration gradients and cutoffs of the x-ray power (the lowest power limit to overcome the Bremsstrahlung radiation losses) are characterized in terms of the lattice constants, unit cell sizes, and photon energies. The parametric analysis indicates that the required x-ray power can be reduced to an order of megawatt by replacing crystals with CNTs. Eventually, the equivalent dielectric approximation of a multi-wall nanotube shows that 250–810 MeV muons can be synchronously coupled with x-rays of 0.65–1.32 keV in the accelerating structure.

  13. Protein structure validation and analysis with X-ray crystallography.

    Science.gov (United States)

    Papageorgiou, Anastassios C; Mattsson, Jesse

    2014-01-01

    X-ray crystallography is the main technique for the determination of protein structures. About 85 % of all protein structures known to date have been elucidated using X-ray crystallography. Knowledge of the three-dimensional structure of proteins can be used in various applications in biotechnology, biomedicine, drug design, and basic research and as a validation tool for protein modifications, ligand binding, and structural authenticity. Moreover, the requirement for pure, homogeneous, and stable protein solutions in crystallizations makes X-ray crystallography beneficial in other fields of protein research as well. Here, we describe the technique of X-ray protein crystallography and the steps involved for a successful three-dimensional crystal structure determination.

  14. Structural analysis of actinidin and a comparison of cadmium and sulfur anomalous signals from actinidin crystals measured using in-house copper- and chromium-anode X-ray sources.

    Science.gov (United States)

    Yogavel, Manickam; Nithya, Nirmal; Suzuki, Atsuo; Sugiyama, Yasuo; Yamane, Takashi; Velmurugan, Devadasan; Sharma, Amit

    2010-12-01

    The structure of the 24 kDa cysteine protease saru-actinidin from the fruit of Actinidia arguta Planch. (sarunashi) was determined by the cadmium/sulfur-SAD method with X-ray diffraction data collected using in-house Cu Kα and Cr Kα radiation. The anomalous scatterers included nine sulfurs and several cadmium ions from the crystallization solution. The high quality of the diffraction data, the use of chromium-anode X-ray radiation and the substantial anomalous signal allowed structure determination and automated model building despite both a low solvent content (analysis and comparison of the sulfur/cadmium anomalous signals at the Cu Kα and Cr Kα wavelengths was carried out. It is proposed that the inclusion of cadmium salts in crystallization solutions coupled with chromium-anode radiation can provide a convenient route for structure determination.

  15. Three-dimensional analysis of vesicle and crystal fragment textures in pumice using high-resolution X-ray CT: Textural evidence of eruptive processes

    Science.gov (United States)

    Ketcham, R. A.; Gardner, J. E.; Abbott, S.

    2011-12-01

    Three-dimensional analysis of high-resolution X-ray computed tomographic (CT) imagery of pumice from Popocatépetl Volcano in central Mexico yields fresh insights into processes of vesicle formation and coalescence and crystal fragmentation that occur during explosive volcanism. Six ~2 cm pumice fragments of varying bulk vesicularity were imaged at ~20 μm resolution. Three-dimensional blob and fabric analysis quantitatively document textural features, and visualization facilitated contextualization of measurements and overall interpretation. Vesicles range in size from mm-scale to below the resolution of the scan data. By comparing the whole-sample 3D vesicle size distributions derived from CT with more detailed distributions from sub-volumes obtained by standard petrographic analysis, we can discern two distinct, roughly log-normal populations in each sample. Vesicles in all samples have preferred orientations, and fabric analysis based on the star volume distribution and displayed as 3D rose diagrams documents a range of preferred shapes from elongate to flattened. Aspect ratios range from 1 to 6, and converge to values of ~2-3 with increasing size. Surface to volume ratios show increasing departure from sphericity with increasing size, which is probably attributable in large part to irregular shapes caused by coalescence. The vesicle fabric was strongest in the highest-vesicularity sample. Some pumices showed evidence of welding or poor mixing between two or more differently devolatilized portions of melt. Interfaces are in some cases apparently welded, with low-vesicularity glass contact zones, and in others are simply sub-planar intersections between distinct glasses. In one instance of the latter, correlated vesicle and phenocryst orientations across both melt portions and not parallel to their interface suggests that their juxtaposition took place before final eruption, while there was still time for fabric development. The pumices show abundant evidence of

  16. Crystallization and X-ray analysis of the T = 4 particle of hepatitis B capsid protein with an N-terminal extension

    Energy Technology Data Exchange (ETDEWEB)

    Tan, Wen Siang [Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor (Malaysia); McNae, Iain W.; Ho, Kok Lian; Walkinshaw, Malcolm D., E-mail: m.walkinshaw@ed.ac.uk [Institute of Structural and Molecular Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, King’s Buildings, Mayfield Road, Edinburgh EH9 3JR,Scotland (United Kingdom); Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor (Malaysia)

    2007-08-01

    Hepatitis B virus capsids have significant potential as carriers for immunogenic peptides. The crystal structure of the T = 4 particle of hepatitis B core protein containing an N-terminal extension reveals that the fusion peptide is exposed on the exterior of the particle. Hepatitis B core (HBc) particles have been extensively exploited as carriers for foreign immunological epitopes in the development of multicomponent vaccines and diagnostic reagents. Crystals of the T = 4 HBc particle were grown in PEG 20 000, ammonium sulfate and various types of alcohols. A temperature jump from 277 or 283 to 290 K was found to enhance crystal growth. A crystal grown using MPD as a cryoprotectant diffracted X-rays to 7.7 Å resolution and data were collected to 99.6% completeness at 8.9 Å. The crystal belongs to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 352.3, b = 465.5, c = 645.0 Å. The electron-density map reveals a protrusion that is consistent with the N-terminus extending out from the surface of the capsid. The structure presented here supports the idea that N-terminal insertions can be exploited in the development of diagnostic reagents, multicomponent vaccines and delivery vehicles into mammalian cells.

  17. Purification, crystallization and preliminary X-ray diffraction experiment of nattokinase from Bacillus subtilis natto.

    Science.gov (United States)

    Yanagisawa, Yasuhide; Chatake, Toshiyuki; Chiba-Kamoshida, Kaori; Naito, Sawa; Ohsugi, Tadanori; Sumi, Hiroyuki; Yasuda, Ichiro; Morimoto, Yukio

    2010-12-01

    Nattokinase is a single polypeptide chain composed of 275 amino acids (molecular weight 27,724) which displays strong fibrinolytic activity. Moreover, it can activate other fibrinolytic enzymes such as pro-urokinase and tissue plasminogen activator. In the present study, native nattokinase from Bacillus subtilis natto was purified using gel-filtration chromatography and crystallized to give needle-like crystals which could be used for X-ray diffraction experiments. The crystals belonged to space group C2, with unit-cell parameters a=74.3, b=49.9, c=56.3 Å, β=95.2°. Diffraction images were processed to a resolution of 1.74 Å with an Rmerge of 5.2% (15.3% in the highest resolution shell) and a completeness of 69.8% (30.0% in the highest resolution shell). This study reports the first X-ray diffraction analysis of nattokinase.

  18. Crystal structure of Pigment Red 254 from X-ray powder diffraction data

    Directory of Open Access Journals (Sweden)

    Svetlana N. Ivashevskaya

    2017-04-01

    Full Text Available The crystal structure of Pigment Red 254 [P.R. 254, C18H10Cl2N2O2; systematic name: 3,6-bis(4-chlorophenyl-2,5-dihydropyrrolo[3,4-c]pyrrole-1,4-dione] was solved from laboratory X-ray powder diffraction data using the simulated annealing method followed by Rietveld refinement because the very low solubility of the pigment in all solvents impedes the growth of single crystals suitable for X-ray analysis. The molecule lies across an inversion center. The dihedral angle between the benzene ring and the pyrrole ring in the unique part of the molecule is 11.1 (2°. In the crystal, molecules are linked via N—H...O hydrogen bonds, forming chains along [110] incorporating R22(8 rings.

  19. Material analysis with X-ray microdiffraction

    Energy Technology Data Exchange (ETDEWEB)

    Friedel, F.; Winkler, U.; Holtz, B. [ThyssenKrupp Stahl AG, Duisburg (Germany); Seyrich, R.; Ullrich, H.J. [Dresden University of Technology (Germany)

    2005-01-01

    Steel has continued to develop its status as a lightweight construction material for the design of vehicle bodies, most recently with the development of multi-phase steel. With a specific mixture of different phases in the steel microstructure, multi-phase steel combines high stability with good forming capacity. The characterisation of the complex structure of the multi-phase steel represents a challenge for metallurgists. For some years a new generation of X-ray diffractometers with two-dimensional (area) detectors and apparatus for local dissolved measurements are available to customers. This paper reports the applications and advantages of the modern X-ray diffractometry method. (copyright 2005 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  20. Crystallization and preliminary X-ray crystallographic analysis of the GluR0 ligand-binding core from Nostoc punctiforme

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jun Hyuck; Park, Soo Jeong; Rho, Seong-Hwan; Im, Young Jun; Kim, Mun-Kyoung; Kang, Gil Bu; Eom, Soo Hyun, E-mail: eom@gist.ac.kr [Department of Life Science, Gwangju Institute of Science and Technology, Gwangju 500-712 (Korea, Republic of)

    2005-11-01

    The GluR0 ligand-binding core from N. punctiforme was expressed, purified and crystallized in the presence of l-glutamate. A diffraction data set was collected to a resolution of 2.1 Å. GluR0 from Nostoc punctiforme (NpGluR0) is a bacterial homologue of the ionotropic glutamate receptor. The ligand-binding core of NpGluR0 was crystallized at 294 K using the hanging-drop vapour-diffusion method. The l-glutamate-complexed crystal belongs to space group C222{sub 1}, with unit-cell parameters a = 78.0, b = 145.1, c = 132.1 Å. The crystals contain three subunits in the asymmetric unit, with a V{sub M} value of 2.49 Å{sup 3} Da{sup −1}. The diffraction limit of the l-glutamate complex data set was 2.1 Å using synchrotron X-ray radiation at beamline BL-4A of the Pohang Accelerator Laboratory (Pohang, Korea)

  1. Expression, purification, crystallization and preliminary X-ray diffraction analysis of the VP8* sialic acid-binding domain of porcine rotavirus strain OSU

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yang-De, E-mail: zhangyd1960@yahoo.com.cn; Li, Hao [National Hepatobiliary and Enteric Surgery Research Center of The Ministry of Health, Xiangya Hospital, Central South University, Hunan Province (China); Liu, Hui; Pan, Yi-Feng [Biochemistry Laboratory, Institution of Biomedical Engineering, Central South University, Hunan Province (China); National Hepatobiliary and Enteric Surgery Research Center of The Ministry of Health, Xiangya Hospital, Central South University, Hunan Province (China)

    2007-02-01

    Porcine rotavirus strain OSU VP8* domain has been expressed, purified and crystallized. X-ray diffraction data from different crystal forms of the VP8* domain have been collected to 2.65 and 2.2 Å resolution, respectively. The rotavirus outer capsid spike protein VP4 is utilized in the process of rotavirus attachment to and membrane penetration of host cells. VP4 is cleaved by trypsin into two domains: VP8* and VP5*. The VP8* domain is implicated in initial interaction with sialic acid-containing cell-surface carbohydrates and triggers subsequent virus invasion. The VP8* domain from porcine OSU rotavirus was cloned and expressed in Escherichia coli. Different crystal forms (orthorhombic P2{sub 1}2{sub 1}2{sub 1} and tetragonal P4{sub 1}2{sub 1}2) were harvested from two distinct crystallization conditions. Diffraction data have been collected to 2.65 and 2.2 Å resolution and the VP8*{sub 65–224} structure was determined by molecular replacement.

  2. Crystallization and preliminary X-ray diffraction analysis of calexcitin from Loligo pealei: a neuronal protein implicated in learning and memory

    Energy Technology Data Exchange (ETDEWEB)

    Beaven, G. D. E.; Erskine, P. T.; Wright, J. N.; Mohammed, F.; Gill, R.; Wood, S. P. [School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX (United Kingdom); Vernon, J.; Giese, K. P. [Wolfson Institute for Biomedical Research, University College London, Cruciform Building, Gower Street, London WC1E 6BT (United Kingdom); Cooper, J. B., E-mail: j.b.cooper@soton.ac.uk [School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX (United Kingdom)

    2005-10-01

    Recombinant squid calexcitin has been crystallized using the hanging-drop vapour-diffusion technique in the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}. The neuronal protein calexcitin from the long-finned squid Loligo pealei has been expressed in Escherichia coli and purified to homogeneity. Calexcitin is a 22 kDa calcium-binding protein that becomes up-regulated in invertebrates following Pavlovian conditioning and is likely to be involved in signal transduction events associated with learning and memory. Recombinant squid calexcitin has been crystallized using the hanging-drop vapour-diffusion technique in the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}. The unit-cell parameters of a = 46.6, b = 69.2, c = 134.8 Å suggest that the crystals contain two monomers per asymmetric unit and have a solvent content of 49%. This crystal form diffracts X-rays to at least 1.8 Å resolution and yields data of high quality using synchrotron radiation.

  3. Cloning, purification, crystallization and preliminary X-ray crystallographic analysis of the biosynthetic N-acetylornithine aminotransferases from Salmonella typhimurium and Escherichia coli

    Energy Technology Data Exchange (ETDEWEB)

    Rajaram, V.; Prasad, K.; Ratna Prasuna, P.; Ramachandra, N.; Bharath, S. R. [Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012 (India); Savithri, H. S. [Department of Biochemistry, Indian Institute of Science, Bangalore 560 012 (India); Murthy, M. R. N., E-mail: mrn@mbu.iisc.ernet.in [Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012 (India)

    2006-10-01

    Acetylornithine aminotransferases, members of the type I subgroup II family of PLP-dependent enzymes, from S. typhimurium and E. coli have been cloned, overexpressed, purified and crystallized. Acetylornithine aminotransferase (AcOAT) is a type I pyridoxal 5′-phosphate-dependent enzyme catalyzing the conversion of N-acetylglutamic semialdehyde to N-acetylornithine in the presence of α-ketoglutarate, a step involved in arginine metabolism. In Escherichia coli, the biosynthetic AcOAT also catalyzes the conversion of N-succinyl-l-2-amino-6-oxopimelate to N-succinyl-l,l-diaminopimelate, one of the steps in lysine biosynthesis. It is closely related to ornithine aminotransferase. AcOAT was cloned from Salmonella typhimurium and E. coli, overexpressed in E. coli and purified using Ni–NTA affinity column chromatography. The enzymes crystallized in the presence of gabaculine. Crystals of E. coli AcOAT (eAcOAT) only diffracted X-rays to 3.5 Å and were twinned. The crystals of S. typhimurium AcOAT (sAcOAT) diffracted to 1.9 Å and had a dimer in the asymmetric unit. The structure of sAcOAT was solved by the molecular-replacement method.

  4. X-ray spectrometry and X-ray microtomography techniques for soil and geological samples analysis

    Energy Technology Data Exchange (ETDEWEB)

    Kubala-Kukuś, A.; Banaś, D.; Braziewicz, J. [Institute of Physics, Jan Kochanowski University, ul. Świetokrzyska 15, 25-406 Kielce (Poland); Holycross Cancer Center, ul. Artwińskiego 3, 25-734 Kielce (Poland); Dziadowicz, M.; Kopeć, E. [Institute of Physics, Jan Kochanowski University, ul. Świetokrzyska 15, 25-406 Kielce (Poland); Majewska, U. [Institute of Physics, Jan Kochanowski University, ul. Świetokrzyska 15, 25-406 Kielce (Poland); Holycross Cancer Center, ul. Artwińskiego 3, 25-734 Kielce (Poland); Mazurek, M.; Pajek, M.; Sobisz, M.; Stabrawa, I. [Institute of Physics, Jan Kochanowski University, ul. Świetokrzyska 15, 25-406 Kielce (Poland); Wudarczyk-Moćko, J. [Holycross Cancer Center, ul. Artwińskiego 3, 25-734 Kielce (Poland); Góźdź, S. [Holycross Cancer Center, ul. Artwińskiego 3, 25-734 Kielce (Poland); Institute of Public Health, Jan Kochanowski University, IX Wieków Kielc 19, 25-317 Kielce (Poland)

    2015-12-01

    A particular subject of X-ray fluorescence analysis is its application in studies of the multielemental sample of composition in a wide range of concentrations, samples with different matrices, also inhomogeneous ones and those characterized with different grain size. Typical examples of these kinds of samples are soil or geological samples for which XRF elemental analysis may be difficult due to XRF disturbing effects. In this paper the WDXRF technique was applied in elemental analysis concerning different soil and geological samples (therapeutic mud, floral soil, brown soil, sandy soil, calcium aluminum cement). The sample morphology was analyzed using X-ray microtomography technique. The paper discusses the differences between the composition of samples, the influence of procedures with respect to the preparation of samples as regards their morphology and, finally, a quantitative analysis. The results of the studies were statistically tested (one-way ANOVA and correlation coefficients). For lead concentration determination in samples of sandy soil and cement-like matrix, the WDXRF spectrometer calibration was performed. The elemental analysis of the samples was complemented with knowledge of chemical composition obtained by X-ray powder diffraction.

  5. Structural Characterization of Doped GaSb Single Crystals by X-ray Topography

    Energy Technology Data Exchange (ETDEWEB)

    Honnicke, M.G.; Mazzaro, I.; Manica, J.; Benine, E.; M da Costa, E.; Dedavid, B. A.; Cusatis, C.; Huang, X. R.

    2009-09-13

    We characterized GaSb single crystals containing different dopants (Al, Cd and Te), grown by the Czochralski method, by x-ray topography and high angular resolution x-ray diffraction. Lang topography revealed dislocations parallel and perpendicular to the crystal's surface. Double-crystal GaSb 333 x-ray topography shows dislocations and vertical stripes than can be associated with circular growth bands. We compared our high-angular resolution x-ray diffraction measurements (rocking curves) with the findings predicted by the dynamical theory of x-ray diffraction. These measurements show that our GaSb single crystals have a relative variation in the lattice parameter ({Delta}d/d) on the order of 10{sup -5}. This means that they can be used as electronic devices (detectors, for example) and as x-ray monochromators.

  6. X-ray crystal structure and small-angle X-ray scattering of sheep liver sorbitol dehydrogenase

    DEFF Research Database (Denmark)

    Yennawar, Hemant; Møller, Magda; Gillilan, Richard;

    2011-01-01

    The X-ray crystal structure of sheep liver sorbitol dehydrogenase (slSDH) has been determined using the crystal structure of human sorbitol dehydrogenase (hSDH) as a molecular-replacement model. slSDH crystallized in space group I222 with one monomer in the asymmetric unit. A conserved tetramer...... the substrate-binding pocket together with the acetate designed by nature to fit large polyol substrates. The substrate-binding pocket is seen to be in close proximity to the tetramer interface, which explains the need for the structural integrity of the tetramer for enzyme activity. Small-angle X...

  7. Crystallization and X-ray diffraction of crystals formed in water-plasticized amorphous lactose.

    Science.gov (United States)

    Jouppila, K; Kansikas, J; Roos, Y H

    1998-01-01

    Effects of storage time and relative humidity on crystallization and crystal forms produced from amorphous lactose were investigated. Crystallization was observed from time-dependent loss of sorbed water and increasing intensities of peaks in X-ray diffraction patterns. The rate of crystallization increased with increasing storage relative humidity. Lactose crystallized mainly as alpha-lactose monohydrate and anhydrous crystals with alpha- and beta-lactose in a molar ratio of 5:3. The results suggested that the crystal form was defined by the early nucleation process. The crystallization data are important in modeling of crystallization phenomena and prediction of stability of lactose-containing food and pharmaceutical materials.

  8. Optimization of triazine nitriles as rhodesain inhibitors: structure-activity relationships, bioisosteric imidazopyridine nitriles, and X-ray crystal structure analysis with human cathepsin L.

    Science.gov (United States)

    Ehmke, Veronika; Winkler, Edwin; Banner, David W; Haap, Wolfgang; Schweizer, W Bernd; Rottmann, Matthias; Kaiser, Marcel; Freymond, Céline; Schirmeister, Tanja; Diederich, François

    2013-06-01

    The cysteine protease rhodesain of Trypanosoma brucei parasites causing African sleeping sickness has emerged as a target for the development of new drug candidates. Based on a triazine nitrile moiety as electrophilic headgroup, optimization studies on the substituents for the S1, S2, and S3 pockets of the enzyme were performed using structure-based design and resulted in inhibitors with inhibition constants in the single-digit nanomolar range. Comprehensive structure-activity relationships clarified the binding preferences of the individual pockets of the active site. The S1 pocket tolerates various substituents with a preference for flexible and basic side chains. Variation of the S2 substituent led to high-affinity ligands with inhibition constants down to 2 nM for compounds bearing cyclohexyl substituents. Systematic investigations on the S3 pocket revealed its potential to achieve high activities with aromatic vectors that undergo stacking interactions with the planar peptide backbone forming part of the pocket. X-ray crystal structure analysis with the structurally related enzyme human cathepsin L confirmed the binding mode of the triazine ligand series as proposed by molecular modeling. Sub-micromolar inhibition of the proliferation of cultured parasites was achieved for ligands decorated with the best substituents identified through the optimization cycles. In cell-based assays, the introduction of a basic side chain on the inhibitors resulted in a 35-fold increase in antitrypanosomal activity. Finally, bioisosteric imidazopyridine nitriles were studied in order to prevent off-target effects with unselective nucleophiles by decreasing the inherent electrophilicity of the triazine nitrile headgroup. Using this ligand, the stabilization by intramolecular hydrogen bonding of the thioimidate intermediate, formed upon attack of the catalytic cysteine residue, compensates for the lower reactivity of the headgroup. The imidazopyridine nitrile ligand showed

  9. Purification, Crystallization And Preliminary X-Ray Analysis of Aminoglycoside-2 ''-Phosphotransferase-Ic [APH(2 '')-Ic] From Enterococcus Gallinarum

    Energy Technology Data Exchange (ETDEWEB)

    Byrnes, L.J.; /SLAC, SSRL; Badarau, A.; Vakulenko, S.B.; /Notre Dame U.; Smith, C.A.; /SLAC, SSRL

    2009-04-30

    Bacterial resistance to aminoglycoside antibiotics is primarily the result of deactivation of the drugs. Three families of enzymes are responsible for this activity, with one such family being the aminoglycoside phosphotransferases (APHs). The gene encoding one of these enzymes, aminoglycoside-2{double_prime}-phosphotransferase-Ic [APH(2{double_prime})-Ic] from Enterococcus gallinarum, has been cloned and the wild-type protein (comprising 308 amino-acid residues) and three mutants that showed elevated minimum inhibitory concentrations towards gentamicin (F108L, H258L and a double mutant F108L/H258L) were expressed in Escherichia coli and subsequently purified. All APH(2{double_prime})-Ic variants were crystallized in the presence of 14-20%(w/v) PEG 4000, 0.25 M MgCl{sub 2}, 0.1 M Tris-HCl pH 8.5 and 1 mM Mg{sub 2}GTP. The crystals belong to the monoclinic space group C2, with one molecule in the asymmetric unit. The approximate unit-cell parameters are a = 82.4, b = 54.2, c = 77.0 {angstrom}, {beta} = 108.8{sup o}. X-ray diffraction data were collected to approximately 2.15 {angstrom} resolution from an F108L crystal at beamline BL9-2 at SSRL, Stanford, California, USA.

  10. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of SpyCEP, a candidate antigen for a vaccine against Streptococcus pyogenes.

    Science.gov (United States)

    Abate, Francesca; Malito, Enrico; Falugi, Fabiana; Margarit Y Ros, Immaculada; Bottomley, Matthew James

    2013-10-01

    Streptococcus pyogenes (Group A streptococcus; GAS) is an important human pathogen against which an effective vaccine does not yet exist. The S. pyogenes protein SpyCEP (S. pyogenes cell-envelope proteinase) is a surface-exposed subtilisin-like serine protease of 1647 amino acids. In addition to its auto-protease activity, SpyCEP is capable of cleaving interleukin 8 and related chemokines, contributing to GAS immune-evasion strategies. SpyCEP is immunogenic and confers protection in animal models of GAS infections. In order to structurally characterize this promising vaccine candidate, several SpyCEP protein-expression constructs were designed, cloned, produced in Escherichia coli, purified by affinity chromatography and subjected to crystallization trials. Crystals of a selenomethionyl form of a near-full-length SpyCEP ectodomain were obtained. The crystals diffracted X-rays to 3.3 Å resolution and belonged to space group C2, with unit-cell parameters a=139.2, b=120.4, c=104.3 Å, β=111°.

  11. Cloning, expression, crystallization and preliminary X-ray analysis of the XMT and DXMT N-methyltransferases from Coffea canephora (robusta)

    Energy Technology Data Exchange (ETDEWEB)

    McCarthy, Andrew A., E-mail: andrewmc@embl.fr [European Molecular Biology Laboratory, 6 Rue Jules Horowitz, BP 181, 38042 Grenoble (France); Biget, Laurent [Nestlé Research and Development, 101 Avenue Gustave Eiffel, Notre-Dame D’Oe, 37097 Tours (France); Lin, Chenwei [Department of Plant Breeding and Genetics, Department of Plant Biology, Cornell University, Ithaca, NY 14853 (United States); Petiard, Vincent [Nestlé Research and Development, 101 Avenue Gustave Eiffel, Notre-Dame D’Oe, 37097 Tours (France); Tanksley, Steve D. [Department of Plant Breeding and Genetics, Department of Plant Biology, Cornell University, Ithaca, NY 14853 (United States); McCarthy, James G. [Nestlé Research and Development, 101 Avenue Gustave Eiffel, Notre-Dame D’Oe, 37097 Tours (France); European Molecular Biology Laboratory, 6 Rue Jules Horowitz, BP 181, 38042 Grenoble (France)

    2007-04-01

    The genes encoding XMT and DXMT, the enzymes from Coffea canephora (robusta) that catalyse the three independent N-methyl transfer reactions in the caffeine-biosynthesis pathway, have been cloned and the proteins have been expressed in Escherichia coli. Both proteins have been crystallized in the presence of the demethylated cofactor S-adenosyl-l-cysteine (SAH) and substrate (xanthosine for XMT and theobromine for DXMT). Caffeine is a secondary metabolite produced by a variety of plants including Coffea canephora (robusta) and there is growing evidence that caffeine is part of a chemical defence strategy protecting young leaves and seeds from potential predators. The genes encoding XMT and DXMT, the enzymes from Coffea canephora (robusta) that catalyse the three independent N-methyl transfer reactions in the caffeine-biosynthesis pathway, have been cloned and the proteins have been expressed in Escherichia coli. Both proteins have been crystallized in the presence of the demethylated cofactor S-adenosyl-l-cysteine (SAH) and substrate (xanthosine for XMT and theobromine for DXMT). The crystals are orthorhombic, with space group P2{sub 1}2{sub 1}2{sub 1} for XMT and C222{sub 1} for DXMT. X-ray diffraction to 2.8 Å for XMT and to 2.5 Å for DXMT have been collected on beamline ID23-1 at the ESRF.

  12. Cloning, expression, crystallization and preliminary X-ray analysis of the first two Ig domains from human Roundabout 1 (Robo1)

    Energy Technology Data Exchange (ETDEWEB)

    Morlot, Cecile [European Molecular Biology Laboratory, 6 Rue Jules Horowitz, BP 181, 38042 Grenoble (France); Hemrika, Wieger; Romijn, Roland A. [ABC Expression Center, Utrecht University, Padualaan 8, 3584 CH Utrecht (Netherlands); Gros, Piet [Department of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht (Netherlands); Cusack, Stephen, E-mail: cusack@embl.fr; McCarthy, Andrew A., E-mail: cusack@embl.fr [European Molecular Biology Laboratory, 6 Rue Jules Horowitz, BP 181, 38042 Grenoble (France)

    2007-08-01

    Robo1 is a large transmembrane receptor expressed on the axon growth cone. Activation of Robo1 by Slit proteins results in axon repulsion from the midline. Here, the purification and crystallization conditions of first two Ig domains of Robo1 are reported. Activation of Roundabout 1 (Robo1) by Slit proteins results in axon repulsion from the midline. Robo1 is a large transmembrane receptor expressed on the axon growth cone and the minimal Robo1-binding region required for Slit activation has been mapped to the N-terminal Ig1–2 domains. The cDNA encoding the first two Ig domains of Robo1 has been cloned and the protein has been expressed in HEK293 EBNA-1 mammalian cells. Here, the purification and crystallization conditions of this Robo1 construct are reported. The crystals are orthorhombic, space group P2{sub 1}2{sub 1}2, with unit-cell parameters a = 38.8, b = 69.4, c = 103.3 Å and one molecule in the asymmetric unit. X-ray diffraction data have been collected to 2.8 Å resolution on beamline ID29 at the ESRF.

  13. Preparation, crystallization and X-ray diffraction analysis to 1.5 Å resolution of rat cysteine dioxygenase, a mononuclear iron enzyme responsible for cysteine thiol oxidation

    Energy Technology Data Exchange (ETDEWEB)

    Simmons, Chad R. [Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853-8001 (United States); Hao, Quan [MacCHESS at the Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY 14853-8001 (United States); Stipanuk, Martha H., E-mail: mhs6@cornell.edu [Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853-8001 (United States)

    2005-11-01

    Recombinant rat cysteine dioxygenase (CDO) has been expressed, purified and crystallized and X-ray diffraction data have been collected to 1.5 Å resolution. Cysteine dioxygenase (CDO; EC 1.13.11.20) is an ∼23 kDa non-heme iron metalloenzyme that is responsible for the oxidation of cysteine by O{sub 2}, yielding cysteinesulfinate. CDO catalyzes the first step in the conversion of cysteine to taurine, as well as the first step in the catabolism of cysteine to pyruvate plus sulfate. Recombinant rat CDO was heterologously expressed, purified and crystallized. The protein was expressed as a fusion protein bearing a polyhistidine tag to facilitate purification, a thioredoxin tag to improve solubility and a factor Xa cleavage site to permit removal of the entire N-terminus, leaving only the 200 amino acids inherent to the native protein. A multi-step purification scheme was used to achieve >95% purity of CDO. The optimal CDO crystals diffracted to 1.5 Å resolution and belonged to space group P4{sub 3}2{sub 1}2 or P4{sub 1}2{sub 1}2, with unit-cell parameters a = b = 57.55, c = 123.06 Å, α = β = γ = 90°. CDO shows little homology to any other proteins; therefore, the structure of the enzyme will be determined by ab initio phasing using a selenomethionyl derivative.

  14. Purification, crystallization and preliminary X-ray crystallographic studies of Rv3705c from Mycobacterium tuberculosis

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Feifei [East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, People’s Republic of (China); Gao, Feng [Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of (China); Li, Honglin [East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, People’s Republic of (China); Gong, Weimin [Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of (China); Zhou, Lin, E-mail: gdtb-bg@vip.163.com [Center for Tuberculosis Control of Guangdong Province, Guangzhou, People’s Republic of (China); Bi, Lijun, E-mail: gdtb-bg@vip.163.com [East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, People’s Republic of (China)

    2014-07-23

    The cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of Rv3705c from M. tuberculosis are described. The conserved protein Rv3705c from Mycobacterium tuberculosis has been cloned, expressed, purified and crystallized by the sitting-drop vapour-diffusion method using PEG 3350 as a precipitant. The Rv3705c crystals exhibited space group P6{sub 1}22 or P6{sub 5}22, with unit-cell parameters a = b = 198.0, c = 364.1 Å, α = β = 90, γ = 120°, and diffracted to a resolution of 3.3 Å.

  15. Crystallization and preliminary X-ray diffraction studies of ferredoxin reductase from Leptospira interrogans

    Energy Technology Data Exchange (ETDEWEB)

    Nascimento, Alessandro S.; Ferrarezi, Thiago [Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador Saocarlense 400, São Carlos, SP, 13560-970 (Brazil); Catalano-Dupuy, Daniela L.; Ceccarelli, Eduardo A. [Facultad de Ciencias Bioquímicas y Farmacéuticas, Molecular Biology Division, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario (Argentina); Polikarpov, Igor, E-mail: ipolikarpov@if.sc.usp.br [Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador Saocarlense 400, São Carlos, SP, 13560-970 (Brazil)

    2006-07-01

    Crystals adequate for X-ray diffraction analysis have been prepared from L. interrogans ferredoxin-NADP{sup +} reductase. Ferredoxin-NADP{sup +} reductase (FNR) is an FAD-containing enzyme that catalyzes electron transfer between NADP(H) and ferredoxin. Here, results are reported of the recombinant expression, purification and crystallization of FNR from Leptospira interrogans, a parasitic bacterium of animals and humans. The L. interrogans FNR crystals belong to a primitive monoclinic space group and diffract to 2.4 Å resolution at a synchrotron source.

  16. Crystal Structures and Small-angle X-ray Scattering Analysis of UDP-galactopyranose Mutase from the Pathogenic Fungus Aspergillus fumigatus

    Energy Technology Data Exchange (ETDEWEB)

    Dhatwalia, Richa; Singh, Harkewal; Oppenheimer, Michelle; Karr, Dale B.; Nix, Jay C.; Sobrado, Pablo; Tanner, John J. (LBNL); (Missouri); (VPI)

    2015-10-15

    UDP-galactopyranose mutase (UGM) is a flavoenzyme that catalyzes the conversion of UDP-galactopyranose to UDP-galactofuranose, which is a central reaction in galactofuranose biosynthesis. Galactofuranose has never been found in humans but is an essential building block of the cell wall and extracellular matrix of many bacteria, fungi, and protozoa. The importance of UGM for the viability of many pathogens and its absence in humans make UGM a potential drug target. Here we report the first crystal structures and small-angle x-ray scattering data for UGM from the fungus Aspergillus fumigatus, the causative agent of aspergillosis. The structures reveal that Aspergillus UGM has several extra secondary and tertiary structural elements that are not found in bacterial UGMs yet are important for substrate recognition and oligomerization. Small-angle x-ray scattering data show that Aspergillus UGM forms a tetramer in solution, which is unprecedented for UGMs. The binding of UDP or the substrate induces profound conformational changes in the enzyme. Two loops on opposite sides of the active site move toward each other by over 10 {angstrom} to cover the substrate and create a closed active site. The degree of substrate-induced conformational change exceeds that of bacterial UGMs and is a direct consequence of the unique quaternary structure of Aspergillus UGM. Galactopyranose binds at the re face of the FAD isoalloxazine with the anomeric carbon atom poised for nucleophilic attack by the FAD N5 atom. The structural data provide new insight into substrate recognition and the catalytic mechanism and thus will aid inhibitor design.

  17. Time dependence of X-ray polarizability of a crystal induced by an intense femtosecond X-ray pulse

    Directory of Open Access Journals (Sweden)

    A. Leonov

    2014-11-01

    Full Text Available The time evolution of the electron density and the resulting time dependence of Fourier components of the X-ray polarizability of a crystal irradiated by highly intense femtosecond pulses of an X-ray free-electron laser (XFEL is investigated theoretically on the basis of rate equations for bound electrons and the Boltzmann equation for the kinetics of the unbound electron gas. The photoionization, Auger process, electron-impact ionization, electron–electron scattering and three-body recombination have been implemented in the system of rate equations. An algorithm for the numerical solution of the rate equations was simplified by incorporating analytical expressions for the cross sections of all the electron configurations in ions within the framework of the effective charge model. Using this approach, the time dependence of the inner shell populations during the time of XFEL pulse propagation through the crystal was evaluated for photon energies between 4 and 12 keV and a pulse width of 40 fs considering a flux of 1012 photons pulse−1 (focusing on a spot size of ∼1 µm. This flux corresponds to a fluence ranging between 0.8 and 2.4 mJ µm−2. The time evolution of the X-ray polarizability caused by the change of the atomic scattering factor during the pulse propagation is numerically analyzed for the case of a silicon crystal. The time-integrated polarizability drops dramatically if the fluence of the X-ray pulse exceeds 1.6 mJ µm−2.

  18. X-ray diffraction of protein crystal grown in a nano-liter scale droplet in a microchannel and evaluation of its applicability.

    Science.gov (United States)

    Maeki, Masatoshi; Yoshizuka, Saori; Yamaguchi, Hiroshi; Kawamoto, Masahide; Yamashita, Kenichi; Nakamura, Hiroyuki; Miyazaki, Masaya; Maeda, Hideaki

    2012-01-01

    We describe the technical aspects of the in-situ X-ray diffraction of a protein crystal prepared by a nanodroplet-based crystallization method. We were able to obtain diffraction patterns from a crystal grown in a capillary without any manipulation. Especially in our experimental approach, the crystals that moved to the nanodroplet interface were fixed strongly enough to carry out X-ray diffraction measurements that could be attributed to the high surface tension of the nanodroplet. The crystal was damaged by an indirect action of the X-rays because our in-situ X-ray diffraction measurement was carried out in the liquid phase without freezing the crystal; however, the obtained several diffraction patterns were of sufficiently fine quality for the crystal structure factors to be generated. We consider the technical examination presented in this paper to represent a seamless coupling of crystallization to X-ray analysis.

  19. Sensitive X-ray detectors made of methylammonium lead tribromide perovskite single crystals

    NARCIS (Netherlands)

    Wei, Haotong; Fang, Yanjun; Mulligan, Padhraic; Chuirazzi, William; Fang, Hong-Hua; Wang, Congcong; Ecker, Benjamin R.; Gao, Yongli; Loi, Maria Antonietta; Cao, Lei; Huang, Jinsong

    2016-01-01

    The large mobilities and carrier lifetimes of hybrid perovskite single crystals and the high atomic numbers of Pb, I and Br make them ideal for X-ray and gamma-ray detection. Here, we report a sensitive X-ray detector made of methylammonium lead bromide perovskite single crystals. A record-high mobi

  20. Sensitive X-ray detectors made of methylammonium lead tribromide perovskite single crystals

    NARCIS (Netherlands)

    Wei, Haotong; Fang, Yanjun; Mulligan, Padhraic; Chuirazzi, William; Fang, Hong-Hua; Wang, Congcong; Ecker, Benjamin R.; Gao, Yongli; Loi, Maria Antonietta; Cao, Lei; Huang, Jinsong

    2016-01-01

    The large mobilities and carrier lifetimes of hybrid perovskite single crystals and the high atomic numbers of Pb, I and Br make them ideal for X-ray and gamma-ray detection. Here, we report a sensitive X-ray detector made of methylammonium lead bromide perovskite single crystals. A record-high mobi

  1. Multiplicity factor and diffraction geometry factor for single crystal X-ray diffraction analysis and measurement of phase content in cubic GaN/GaAs(001) epilayers

    Institute of Scientific and Technical Information of China (English)

    QU; Bo

    2001-01-01

    [1] Yang, H., Zheng, L.X., Li, J.B. et al., Cubic-phase GaN light-emitting diode, Appl. Phys. Lett., 1999, 74(17): 2498.[2] Trampert, A., Brandt, O., Yang, H. et al., Direct observation of the initial nucleation and epitaxial growth of metastable cubic GaN on GaAs(001), Appl. Phys. Lett., 1997, 70(5): 583.[3] Balakrishnan, K., Feuillet, G., Ohta, K. et al., Structural analysis of cubic GaN through X-ray pole figure generation, Jpn. J. Appl. Phys., 1997, 36(10, part 1): 6221.[4] Basu, S.N., Lei, T., Moustakas, T.D., Microstructures of GaN films deposited on (001) and (111) Si substrates using electron cyclotron resonance assisted-molecular beam epitaxy, J. Mater. Res., 1994, 9(9): 2370.[5] Powell, R.C., Lee, N.E., Kim, Y.W. et al., Heteroepitaxial wurtzite and zinc-blende structure GaN grown by reactive-ion molecular-beam epitaxy: growth kinetics, microstructure, and properties, J. Appl. Phys., 1993, 73(1): 189.[6] Camassel, J., Vicente, P., Planes, N. et al., Experimental investigation of cubic to hexagonal ratio for GaN layers deposited on 3C-SiC/Si, Phys. Stat. Sol. (b), 1999, 216: 253.[7] Sun, X.L., Yang, H., Zheng, L.X., Stability investigation of cubic GaN films grown by MOCVD on GaAs(100), Appl. Phys. Lett., 1999, 74(19 ): 2827.[8] Moret, M., Ruttenach-clur, S., Moreaud, N. et al., MOCVD growth of cubic gallium nitride: effect of V/III ratio, Phys. Stat. Sol. (a), 1999, 176: 493.[9] Qin, Z.X., Nagano, H., Sugure, Y. et al., High-resolution X-ray diffraction analysis of cubic GaN grown on (001)GaAs by RF-radical source molecular beam epitaxy, J. Crys. Growth, 1998, 189/190: 425.[10] Qin Zhixin, Kobayashi, M., Yoshikawa, A., X-ray diffraction reciprocal space and pole figure characterization of cubic GaN epitaxial layers grown on (001)GaAs by molecular beam epitaxy, J. Mater. Sci., 1999,109: 199.[11] Trampert, A., Brandt, O., Ploog, K. H., Phase transformations and phase stability in epitaxial

  2. Purification, crystallization and preliminary X-ray diffraction analysis of the IL-20-IL-20R1-IL-20R2 complex

    Energy Technology Data Exchange (ETDEWEB)

    Logsdon, Naomi J.; Allen, Christopher E.; Rajashankar, Kanagalaghatta R.; Walter, Mark R. (Cornell); (UAB)

    2012-02-08

    Interleukin-20 (IL-20) is an IL-10-family cytokine that regulates innate and adaptive immunity in skin and other tissues. In addition to protecting the host from various external pathogens, dysregulated IL-20 signaling has been shown to contribute to the pathogenesis of human psoriasis. IL-20 signals through two cell-surface receptor heterodimers, IL-20R1-IL-20R2 and IL-22R1-IL-20R2. In this report, crystals of the IL-20-IL-20R1-IL-20R2 ternary complex have been grown from polyethylene glycol solutions. The crystals belonged to space group P4{sub 1}2{sub 1}2 or P4{sub 3}2{sub 1}2, with unit-cell parameters a = 111, c = 135 {angstrom}, and diffracted X-rays to 3 {angstrom} resolution. The crystallographic asymmetric unit contains one IL-20-IL-20R1-IL-20R2 complex, corresponding to a solvent content of approximately 54%.

  3. Non-covalent interactions in 2-methylimidazolium copper(II) complex (MeImH)2[Cu(pfbz)4]: Synthesis, characterization, single crystal X-ray structure and packing analysis

    Science.gov (United States)

    Sharma, Raj Pal; Saini, Anju; Kumar, Santosh; Kumar, Jitendra; Sathishkumar, Ranganathan; Venugopalan, Paloth

    2017-01-01

    A new anionic copper(II) complex, (MeImH)2 [Cu(pfbz)4] (1) where, MeImH = 2-methylimidazolium and pfbz = pentafluorobenzoate has been isolated by reacting copper(II) sulfate pentahydrate, pentafluorobenzoic acid and 2-methylimidazole in ethanol: water mixture in 1:2:2 molar ratio. This complex 1 has been characterized by elemental analysis, thermogravimetric analysis, spectroscopic techniques (UV-Vis, FT-IR) and conductance measurements. The complex salt crystallizes in monoclinic crystal system with space group C2/c. Single crystal X-ray structure determination revealed the presence of discrete ions: [Cu(pfbz)4]2- anion and two 2-methylimidazolium cation (C4H7N2)+. The crystal lattice is stabilized by strong hydrogen bonding and F⋯F interactions between cationic-anionic and the anionic-anionic moieties respectively, besides π-π interactions.

  4. Crystallization, X-ray diffraction analysis and SIRAS/molecular-replacenent phasing of three crystal forms of Anabaena sensory rhodopsin transducer

    Energy Technology Data Exchange (ETDEWEB)

    Vogeley, Lutz; Luecke, Hartmut, E-mail: hudel@uci.edu [University of California, Irvine (United States)

    2006-04-01

    Crystals of Anabaena sensory rhodopsin transducer, the transducer for the cyanobacterial photosensor Anabaena sensory rhodopsin, obtained in the space groups P4, C2 and P2{sub 1}2{sub 1}2{sub 1} diffract to 1.8, 2.1 and 2.0 Å, respectively. Phases for these crystal forms were obtained by SIRAS phasing using an iodide quick-soak derivative (P4) and molecular replacement (C2 and P2{sub 1}2{sub 1}2{sub 1}). Anabaena sensory rhodopsin transducer (ASRT) is a 14.7 kDa soluble signaling protein associated with the membrane-embedded light receptor Anabaena sensory rhodopsin (ASR) from Anabaena sp., a freshwater cyanobacterium. Crystals of ASRT were obtained in three different space groups, P4, C2 and P2{sub 1}2{sub 1}2{sub 1}, which diffract to 1.8, 2.1 and 2.0 Å, respectively. Phases for one of these crystal forms (P4) were obtained by SIRAS phasing using an iodide quick-soak derivative and a partial model was built. Phases for the remaining crystal forms were obtained by molecular replacement using the partial model from the P4 crystal form.

  5. Real-time, high-resolution x-ray diffraction measurements on shocked crystals at a synchrotron facility.

    Science.gov (United States)

    Gupta, Y M; Turneaure, Stefan J; Perkins, K; Zimmerman, K; Arganbright, N; Shen, G; Chow, P

    2012-12-01

    The Advanced Photon Source (APS) at Argonne National Laboratory was used to obtain real-time, high-resolution x-ray diffraction measurements to determine the microscopic response of shock-compressed single crystals. Disk shaped samples were subjected to plane shock wave compression by impacting them with half-inch diameter, flat-faced projectiles. The projectiles were accelerated to velocities ranging between 300 and 1200 m/s using a compact powder gun designed specifically for use at a synchrotron facility. The experiments were designed to keep the sample probed volume under uniaxial strain and constant stress for a duration longer than the 153.4 ns spacing between x-ray bunches. X-rays from a single pulse (crystals at the APS are presented. Analytic developments to determine the effects of crystal substructure and non-ideal geometry on the diffraction pattern position and shape are presented. Representative real-time x-ray diffraction data, indicating shock-induced microstructural changes, are presented for a shock-compressed Al(111) sample. The experimental developments presented here provided, in part, the impetus for the Dynamic Compression Sector (DCS) currently under development at the APS. Both the synchronization∕x-ray detection methods and the analysis equations for high-resolution single crystal x-ray diffraction can be used at the DCS.

  6. In Situ Mineralogical Analysis of Planetary Materials Using X-Ray Diffraction and X-Ray Fluorescence

    Science.gov (United States)

    Sarrazin, P.; Blake, D.; Vaniman, D.; Chang, Sherwood (Technical Monitor)

    1996-01-01

    Remote observations of Mars have led scientists to believe that its early climate was similar to that of the early Earth, having had abundant liquid water and a dense atmosphere. One of the most fascinating questions of recent times is whether simple bacterial life developed on Mars (as it did on the Earth) during this early element period. Analyses of SNC meteorites have broadened considerably our knowledge of the chemistry of certain types of Martian rocks, underscoring the tantalizing possibility of early hydrothermal systems and even of ancient bacterial life. Detailed analyses of SNC meteorites in Terrestrial laboratories utilize the most sophisticated organic, isotopic and microscopic techniques in existence. Indeed; it is unlikely that the key biogenic indicators used in McKay et al (ibid) could be identified by a remote instrument on the surface of Mars. As a result, it is probable that any robotic search for evidence of an ancient Martian biosphere will have as its focus the identification of key minerals in likely host rocks rather than the direct detection of organic or isotopic biomarkers. Even on a sample return mission, mineralogical screening will be utilized to choose the most likely candidate rocks. X-ray diffraction (XRD) is the only technique that can provide a direct determination of the crystal structures of the phases present within a sample. When many different crystalline phases are present, quantitative analysis is better constrained if used in conjunction with a determination of elemental composition, obtainable by X-ray fluorescence (XRF) using the same X-ray source as for XRD. For planetary surface analysis, a remote instrument combining XRD and XRF could be used for mineralogical characterization of both soils and rocks. We are designing a remote XRD/XRF instrument with this objective in mind. The instrument concept pays specific attention to constraints in sample preparation, weight, volume, power, etc. Based on the geometry of a

  7. Numerical Modeling on Thermal Loading of Diamond Crystal in X-ray FEL Oscillator

    CERN Document Server

    Song, Meiqi; Guo, Yuhang; Li, Kai; Deng, Haixiao

    2015-01-01

    Due to high reflectivity and high resolution to X-ray pulse, diamond is one of the most popular Bragg crystals serving as the reflecting mirror and mono-chromator in the next generation free electrons lasers (FELs). The energy deposition of X-rays will result in thermal heating, and thus lattice expanding of diamond crystal, which may degrade the performance of X-ray FELs. In this paper, the thermal loading effect of diamond crystal for X-ray FEL oscillator has been systematically studied by the combined simulation of Geant4 and ANSYS, and its dependence on the environment temperature, crystal size, X-ray pulse repetition rate and pulse energy are presented.

  8. Incommensurate modulations in Bi-2212 high-T_c superconductor revealed by single-crystal X-ray analysis using direct methods

    Institute of Scientific and Technical Information of China (English)

    付正清; 李阳; 程庭柱; 张裕恒; 顾秉林; 范海福

    1995-01-01

    The incommensurate modulated structure of the Bi2Sr2Ca1Cu2Oy high-Tc superocnductor has been studied by direct methods with X-ray diffraction data from a single crystal. The super-space group is N111Bbmb with three-dimensional unit cell parameters a = 0.54222 nm, b=0.5437 nm, c=3.0537 run, α=β=γ=90° andthemodula-tion wave vector q=(0, 0.22, 1). 543 main reflections, 867 first-order and 469 second-order satellite reflections have been observed. Phases of main reflections are derived by a conventional direct-method program SAPI91. The phases of satellite reflections are derived by the program DIMS running with default control based on the known phases of main reflections. The atomic parameters of the basic structure and of the modulation so obtained consist with the results from other authors. For the first time the structure details of the incommensurate modulation in the Bi-2212 phase are observed directly without relying on any assumed model of modulation.

  9. Improving Protein Crystal Quality by the Without-Oil Microbatch Method: Crystallization and Preliminary X-ray Diffraction Analysis of Glutathione Synthetase from Pseudoalteromonas haloplanktis

    Directory of Open Access Journals (Sweden)

    Antonella Albino

    2011-09-01

    Full Text Available Glutathione synthetases catalyze the ATP-dependent synthesis of glutathione from L-γ-glutamyl-L-cysteine and glycine. Although these enzymes have been sequenced and characterized from a variety of biological sources, their exact catalytic mechanism is not fully understood and nothing is known about their adaptation at extremophilic environments. Glutathione synthetase from the Antarctic eubacterium Pseudoalteromonas haloplanktis (PhGshB has been expressed, purified and successfully crystallized. An overall improvement of the crystal quality has been obtained by adapting the crystal growth conditions found with vapor diffusion experiments to the without-oil microbatch method. The best crystals of PhGshB diffract to 2.34 Å resolution and belong to space group P212121, with unit-cell parameters a = 83.28 Å, b = 119.88 Å, c = 159.82 Å. Refinement of the model, obtained using phases derived from the structure of the same enzyme from Escherichia coli by molecular replacement, is in progress. The structural determination will provide the first structural characterization of a psychrophilic glutathione synthetase reported to date.

  10. Phase Sensitive X-Ray Diffraction Imaging Study of Protein Crystals

    Science.gov (United States)

    Hu, Z. W.

    2003-01-01

    The study of defects and growth of protein crystals is of importance in providing a fundamental understanding of this important category of systems and the rationale for crystallization of better ordered crystals for structural determination and drug design. Yet, as a result of the extremely weak scattering power of x-rays in protein and other biological macromolecular crystals, the extinction lengths for those crystals are extremely large and, roughly speaking, of the order of millimeters on average compared to the scale of micrometers for most small molecular crystals. This has significant implication for x-ray diffraction and imaging study of protein crystals, and presents an interesting challenge to currently available x-ray analytical techniques. We proposed that coherence-based phase sensitive x-ray diffraction imaging could provide a way to augment defect contrast in x-ray diffraction images of weakly diffracting biological macromolecular crystals. I shall examine the principles and ideas behind this approach and compare it to other available x-ray topography and diffraction methods. I shall then present some recent experimental results in two model protein systems-cubic apofemtin and tetragonal lysozyme crystals to demonstrate the capability of the coherence-based imaging method in mapping point defects, dislocations, and the degree of perfection of biological macromolecular crystals with extreme sensitivity. While further work is under way, it is intended to show that the observed new features have yielded important information on protein crystal perfection and nucleation and growth mechanism otherwise unobtainable.

  11. Theoretical concepts of X-ray nanoscale analysis theory and applications

    CERN Document Server

    Benediktovitch, Andrei; Ulyanenkov, Alexander

    2013-01-01

    This book provides a concise survey of modern theoretical concepts of X-ray materials analysis. The principle features of the book are: basics of X-ray scattering, interaction between X-rays and matter and new theoretical concepts of X-ray scattering. The various X-ray techniques are considered in detail: high-resolution X-ray diffraction, X-ray reflectivity, grazing-incidence small-angle X-ray scattering and X-ray residual stress analysis. All the theoretical methods presented use the unified physical approach. This makes the book especially useful for readers learning and performing data ana

  12. Crystallization and X-ray Crystallographic Analysis of the Adhesive SpaC Pilin Subunit in the SpaCBA Pilus of Gut-adapted Lactobacillus rhamnosus GG.

    Science.gov (United States)

    Kant, Abhiruchi; von Ossowski, Ingemar; Palva, Airi; Krishnan, Vengadesan

    2016-01-01

    Gram-positive Lactobacillus rhamnosus GG, a gut-adapted commensalic (and probiotic) strain, is known to express sortase-assembled pili on its cell surface. These SpaCBA-called pili consist of three different types of building blocks; the SpaA backbone-pilin subunit and the SpaB and SpaC ancillary pilins. SpaC is a relatively large (~90kDa) multi-domain fimbrial adhesin, and while it is located primarily at the SpaCBA pilus tip, occasionally, it can also be detected throughout the length of pilus backbone. Functionally, SpaC mainly accounts for SpaCBA pilus-mediated interactions with intestinal mucus, collagen, and human gut epithelial cells. Moreover, SpaC adhesiveness is also perceived to have a causal relationship with SpaCBA pilus-induced host-cell immune responses. In order to improve the mechanistic understanding of SpaC and its adhesive properties by structural investigation, we purified and successfully crystallized a recombinant construct of the near full-length SpaC protein (residues 36-856) in the presence of magnesium ions. X-ray diffraction data were collected to 2.6 Å resolution. The SpaC crystal belongs to the space group P21212 with unit cell parameters a = 116.5, b = 128.3, c = 136.5 Å and contains two molecules in the asymmetric unit. Presence of conserved metal ion-dependent adhesion site containing von Willebrand factor type A domain suggests its likely role in the function of SpaC.

  13. Simultaneous analysis of Grazing Incidence X-Ray reflectivity and X-ray standing waves from periodic multilayer systems

    NARCIS (Netherlands)

    Yakunin, S.N.; Makhotkin, I.; Chuyev, M.A.; Seregin, A.Y.; Pashayev, E.M.; Louis, E.; Kruijs, van de R.W.E.; Bijkerk, F.; Kovalchuk, M.V.

    2012-01-01

    Structural analysis of periodic multilayers with small period thickness (~4 nm) is a challenging task, especially when thicknesses of intermixed interfaces become comparable to individual layer thicknesses. In general, angular dependent X-ray fluorescence measurements, excited by the X-ray standing

  14. Determination of inconsistency of crystal lattice parameters of. gamma. - and. gamma. '-phases of nickel heat resisting alloys by Fourier-analysis of x-ray diffraction reflex profiles

    Energy Technology Data Exchange (ETDEWEB)

    Samojlov, A.I.; Ignatova, I.A.; Krivko, A.I.; Kozlova, V.S.; Dodonova, L.P.

    1983-01-01

    A method is outlined that enables with the use of Fourier-analysis of summary unresolved X-ray diffraction profile of the matrix ..gamma.. and intermetallic ..gamma..' phases of nickel heat resisting alloys of the Ni-Cr-Co-Al-Ti-Nb-W-Mo-V -Hf system, to calculate the location of reflexes of each phase, that is, to determine the periods of their crystal lattices in the alloy (in monolith) directly without electrolytic separation of ..gamma..'-phase. The limits of the method applicability were determined.

  15. Flat Crystal x-ray Spectrometer for Quantitative Spectral Measurement in the 2-5 keV Region

    Institute of Scientific and Technical Information of China (English)

    ZHAO Yang; ZHANG Ji-Yan; YANG Jia-Min; WEI Min-Xi; DENG Bo; ZHU Tuo; HU Zhi-Min; XIONG Gang; SHANG Wan-Li; KUANG Long-Yu; YANG Guo-Hong

    2011-01-01

    @@ A technique of fiat crystal x-ray spectrometer for quantitative spectral measurement is described.For the flat crystal spectrograph geometry, the quantitative reduction of relating the CCD counts back to the photon flux from the x-ray source is established.The absolute calibrations of the integral diffraction coefficients of the crystal and the CCD sensitivity make it possible to measure absolute photons flux within the energy range of 2000-5000 eV.The uncertainty analysis of the calibrations is carried out to obtain the energy resolved uncertainties of crystal and CCD.Thus, the experimentai spectra with spectral resolved intensity uncertainties are available.Then, a performing experiment of laser-produced Ti plasma is carried out and the absolute x-ray spectra with intensity uncertainty less than 8.5% are obtained.The technique is promising for absolute spectral measurement of high temperature plasmas in a kilo-electron-volt region.

  16. TES X-ray microcalorimeters for X-ray astronomy and material analysis

    Science.gov (United States)

    Mitsuda, Kazuhisa

    2016-11-01

    TES X-ray microcalorimeter arrays provide not only high-energy resolution (FWHM spectroscopy but also imaging and high-counting-rate capabilities. They are very promising spectrometer for X-ray astronomy and material analysis. In this paper, we report our recent progress. For material analysis, we have fabricated 8 × 8 format array with a fast signal response ( 40 μs) and proved the energy resolution of 5.8 eV FWHM at 5.9 keV. We developed common biasing scheme to reduce number of wirings from room temperature to the cryogenic stage. From measurements using the newly-designed common-bias SQUID array amplifier chips, and from numerical simulations, we demonstrated that signal cross talks due to the common bias is enough small. For space applications, we are developing frequency-division signal multiplexing system. We have fabricated a baseband feedback system and demonstrated that the noise added by the feedback system is about 4 eV FWHM equivalent for 16 ch multiplexing system. The digital to analog converter (DAC) dominates the noise, and needs be reduced by a factor of four for future astronomy missions.

  17. Purification, crystallization and preliminary X-ray crystallographic analysis of ST1022, a putative member of the Lrp/AsnC family of transcriptional regulators isolated from Sulfolobus tokodaii strain 7

    Energy Technology Data Exchange (ETDEWEB)

    Nakano, Noboru; Kumarevel, Thirumananseri, E-mail: tskvel@spring8.or.jp; Matsunaga, Emiko; Shinkai, Akeo [RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148 (Japan); Kuramitsu, Seiki [RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148 (Japan); Department of Biological Sciences, Graduate School of Science, Osaka University, Tayonaka, Osaka 560-0043 (Japan); Yokoyama, Shigeyuki, E-mail: tskvel@spring8.or.jp [RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148 (Japan); Genomic Sciences Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045 (Japan); Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan)

    2007-11-01

    A putative member of the Lrp/AsnC family of transcriptional regulators, ST1022 from S. tokodaii strain 7, has been purified and crystallized in the absence and presence of the effector l-glutamine. A molecular-replacement solution was found using the FL11 transcriptional regulator from Pyrococcus sp. OT3 as a model and structural refinement is under way. The Lrp/AsnC family of transcriptional regulators, also known as feast/famine transcriptional regulators, are widely distributed among bacteria and archaea. This family of proteins are likely to be involved in cellular metabolism, with exogenous amino acids functioning as effectors. Here, the crystallization and preliminary X-ray diffraction analysis of ST1022, a member of the Lrp/AsnC family of proteins, is reported with and without exogenous glutamine as the effector molecule. The crystals of native ST1022 and of the putative complex belong to the tetragonal space group I422, with unit-cell parameters a = b = 103.771, c = 73.297 Å and a = b = 103.846, c = 73.992 Å, respectively. Preliminary X-ray diffraction data analysis and molecular-replacement solution revealed the presence of one monomer per asymmetric unit.

  18. Crystallization Dynamics of Organolead Halide Perovskite by Real-Time X-ray Diffraction.

    Science.gov (United States)

    Miyadera, Tetsuhiko; Shibata, Yosei; Koganezawa, Tomoyuki; Murakami, Takurou N; Sugita, Takeshi; Tanigaki, Nobutaka; Chikamatsu, Masayuki

    2015-08-12

    We analyzed the crystallization process of the CH3NH3PbI3 perovskite by observing real-time X-ray diffraction immediately after combining a PbI2 thin film with a CH3NH3I solution. A detailed analysis of the transformation kinetics demonstrated the fractal diffusion of the CH3NH3I solution into the PbI2 film. Moreover, the perovskite crystal was found to be initially oriented based on the PbI2 crystal orientation but to gradually transition to a random orientation. The fluctuating characteristics of the crystallization process of perovskites, such as fractal penetration and orientational transformation, should be controlled to allow the fabrication of high-quality perovskite crystals. The characteristic reaction dynamics observed in this study should assist in establishing reproducible fabrication processes for perovskite solar cells.

  19. Antiferroelectric surface layers in a liquid crystal as observed by synchrotron x-ray scattering

    DEFF Research Database (Denmark)

    Gramsbergen, E. F.; de Jeu, W. H.; Als-Nielsen, Jens Aage

    1986-01-01

    The X-ray reflectivity form the surface of a liquid crystal with terminally polar (cyano substituted) molecules has been studied using a high-resolution triple-axis X-ray spectrometer in combination with a synchrotron source. It is demonstrated that at the surface of the smectic Al phase a few...

  20. An X-ray luminosity analysis for FRIs and FRIIs

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Radio galaxies are divided into two groups according to their luminosities at 178 MHz, namely Fa- naroff-Riley type Is (FRIs) and Fanaroff-Riley type IIs (FRIIs) with FRIs showing lower radio luminosities than FRIIs. In this paper, the X-ray data are compiled for 183 radio galaxies (61 FRIs and 122 FRIIs), from the available literature, for the analysis of the X-ray properties. The 1 keV X-ray luminosities are calculated and discussed for the two groups, and an averaged X-ray luminosity of logLX1 keV = 41.30±2.51 erg·s-1·keV-1 is found for FRIs, which is lower than that for FRIIs, logLX1 KeV = 43.39±3.06 erg·s-1·keV-1. A Kolmogorov-Smirnov (K-S) test indicates that the probability for the X-ray luminosity distributions of the two groups to be from the same parent distribution is 1.44×10-10. We also discuss the origin and the mechanism of the X-ray emission for FRIs and FRIIs.

  1. An X-ray luminosity analysis for FRIs and FRIIs

    Institute of Scientific and Technical Information of China (English)

    ZHANG ChunLing; FAN dunHui

    2009-01-01

    Radio galaxies are divided into two groups according to their luminosities at 178 MHz,namely Fa-naroff-Riley type Is (FRIIs) and Fanaroff-Riley type IIs (FRIIs) with FRIs showing lower radio luminosities than FRIIs.In this paper,the X-ray data are compiled for 183 radio galaxies (61 FRIs and 122 FRIIs),from the available literature,for the analysis of the X-ray properties.The 1 keV X-ray luminosities are calculated and discussed for the two groups,and an averaged X-ray luminosity of logLx1 keV= 41.30±2.51 erg· s-1.keV-1 is found for FRIs,which is lower than that for FRIIs,logLx1 KeV= 43.39±3.06 erg·s-1 keV-1.A Kolmogorov-Smirnov (K-S) test indicates that the probability for the X-ray luminosity distributions of the two groups to be from the same parent distribution is 1.44×1010.We also discuss the origin and the mechanism of the X-ray emission for FRIs and FRIIs.

  2. An X-ray luminosity analysis for FRIs and FRIIs

    Science.gov (United States)

    Zhang, Chunling; Fan, Junhui

    2009-09-01

    Radio galaxies are divided into two groups according to their luminosities at 178 MHz, namely Fanaroff-Riley type Is (FRIs) and Fanaroff-Riley type IIs (FRIIs) with FRIs showing lower radio luminosities than FRIIs. In this paper, the X-ray data are compiled for 183 radio galaxies (61 FRIs and 122 FRIIs), from the available literature, for the analysis of the X-ray properties. The 1 keV X-ray luminosities are calculated and discussed for the two groups, and an averaged X-ray luminosity of log L {X/1 keV} = 41.30±2.51 erg·s-1·keV-1 is found for FRIs, which is lower than that for FRIIs, log L {X/1 keV} = 43.39±3.06 erg·s-1·keV-1. A Kolmogorov-Smirnov (K-S) test indicates that the probability for the X-ray luminosity distributions of the two groups to be from the same parent distribution is 1.44×10-10. We also discuss the origin and the mechanism of the X-ray emission for FRIs and FRIIs.

  3. Crystal optics for hard-X-ray spectroscopy of highly charged ions

    OpenAIRE

    Beyer, H. F.; Attia, D.; Banas, D; Bigot, E. -O. Le; Bosch, F.; Dousse, Jean-Claude; Förster, E.; Gumberidze, A.; Hagmann, S.; Heß, S.; J. Hoszowska; Indelicato, P.; Jagodzinski, P.; Kozhuharov, Chr.; Krings, Th.

    2009-01-01

    A twin crystal-spectrometer assembly, operated in the focusing compensated asymmetric Laue geometry has been developed for accurate spectroscopy of fast highly charged heavy ions in the hard-X-ray region. Coupled to the focusing crystal optics is a specially developed two-dimensional position-sensitive X-ray detector which is necessary for retaining spectral resolution also for fast moving sources. We summarize the crystal optics and demonstrate the usefulness of the instrument for spectrosco...

  4. The rotating-crystal method in femtosecond X-ray diffraction.

    Science.gov (United States)

    Freyer, B; Stingl, J; Zamponi, F; Woerner, M; Elsaesser, T

    2011-08-01

    We report the first implementation of the rotating-crystal method in femtosecond X-ray diffraction. Applying a pump-probe scheme with 100 fs hard X-ray probe pulses from a laser-driven plasma source, the novel technique is demonstrated by mapping structural dynamics of a photoexcited bismuth crystal via changes of the diffracted intensity on a multitude of Bragg reflections. The method is compared to femtosecond powder diffraction and to Bragg diffraction from a crystal with stationary orientation.

  5. High-resolution X-ray microdiffraction analysis of natural teeth

    Energy Technology Data Exchange (ETDEWEB)

    Xue, Jing; Zhang, Linling; Zou, Ling; Liao, Yunmao; Li, Jiyao; Xiao, Liying; Li, Wei, E-mail: leewei2000@sina.com [State Key Laboratory of Oral Diseases, Sichuan University, People’s Republic of (China)

    2008-05-01

    In situ microzone X-ray diffraction analysis of natural teeth is presented. From our experiment, layer orientation and continuous crystal variations in teeth could be conveniently studied using fast online measurements by high-resolution X-ray microdiffraction equipment. The main component of natural teeth was determined many years ago as calcium phosphate, mostly in the form of hydroxyapatite with different crystallites. In the past, the method used in tooth crystal investigation has been mainly powder X-ray diffraction analysis, but this method has its drawbacks, i.e. the destruction of the natural tooth structure and the difficulty in examining the preferred orientation in different layers of the tooth. During the last century, microzone X-ray diffraction on the tooth surface was carried out, but, as the technology was less sophisticated, the results obtained were not very detailed. The newly developed microdiffraction equipment permits analysis of the microzone of teeth in situ. To test this new microdiffraction equipment, microdiffraction analysis of one natural healthy deciduous molar tooth and one carious deciduous molar tooth has been performed, using a Bruker D8 instrument. Phase analysis of the two teeth was performed; the crystal size at six test points in the natural healthy tooth was calculated by reflection (211), and the crystal preferred orientation of reflection (300) and reflection (002) at six test points in the natural healthy tooth were compared. The results showed that the tooth was a kind of biological mixed crystal composed of several crystal phases, the main crystal phase being hydroxyapatite. The crystal size grew larger going from the dentin to the enamel. The crystal preferred orientation mainly existed in the enamel, especially in the reflection (002). From our experiment, layer orientation and continuous crystal variations in teeth could be conveniently studied using fast online measurements by high-resolution X-ray microdiffraction

  6. X-ray structure analysis of a metalloprotein with enhanced active-site resolution using in situ x-ray absorption near edge structure spectroscopy.

    Science.gov (United States)

    Arcovito, Alessandro; Benfatto, Maurizio; Cianci, Michele; Hasnain, S Samar; Nienhaus, Karin; Nienhaus, G Ulrich; Savino, Carmelinda; Strange, Richard W; Vallone, Beatrice; Della Longa, Stefano

    2007-04-10

    X-ray absorption spectroscopy is exquisitely sensitive to the coordination geometry of an absorbing atom and therefore allows bond distances and angles of the surrounding atomic cluster to be measured with atomic resolution. By contrast, the accuracy and resolution of metalloprotein active sites obtainable from x-ray crystallography are often insufficient to analyze the electronic properties of the metals that are essential for their biological functions. Here, we demonstrate that the combination of both methods on the same metalloprotein single crystal yields a structural model of the protein with exceptional active-site resolution. To this end, we have collected an x-ray diffraction data set to 1.4-A resolution and Fe K-edge polarized x-ray absorption near edge structure (XANES) spectra on the same cyanomet sperm whale myoglobin crystal. The XANES spectra were quantitatively analyzed by using a method based on the multiple scattering approach, which yielded Fe-heme structural parameters with +/-(0.02-0.07)-A accuracy on the atomic distances and +/-7 degrees on the Fe-CN angle. These XANES-derived parameters were subsequently used as restraints in the crystal structure refinement. By combining XANES and x-ray diffraction, we have obtained an cyanomet sperm whale myoglobin structural model with a higher precision of the bond lengths and angles at the active site than would have been possible with crystallographic analysis alone.

  7. Purification, crystallization and preliminary X-ray analysis of bifunctional isocitrate dehydrogenase kinase/phosphatase in complex with its substrate, isocitrate dehydrogenase, from Escherichia coli

    OpenAIRE

    2009-01-01

    The protein complex of bifunctional isocitrate dehydrogenase kinase/phosphatase with its substrate, isocitrate dehydrogenase, has been crystallized for structural analysis. A complete data set was collected from the complex crystal and processed to 2.9 Å resolution.

  8. Crystallization and preliminary X-ray studies of mouse centrin1

    Energy Technology Data Exchange (ETDEWEB)

    Park, Jung Hee [Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Ziegelstrasse 5-9, D-10098 Berlin (Germany); Krauss, Norbert [Institut für Biochemie, Charité - Universitätsmedizin Berlin, Monbijoustrasse 2, D-10117 Berlin (Germany); Pulvermüller, Alexander [Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Ziegelstrasse 5-9, D-10098 Berlin (Germany); Scheerer, Patrick; Höhne, Wolfgang [Institut für Biochemie, Charité - Universitätsmedizin Berlin, Monbijoustrasse 2, D-10117 Berlin (Germany); Giessl, Andreas; Wolfrum, Uwe [Zell- und Matrixbiologie, Institut für Zoologie, Johannes Gutenberg-Universität Mainz, D-55099 Mainz (Germany); Hofmann, Klaus Peter, E-mail: kph@charite.de; Ernst, Oliver Peter [Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Ziegelstrasse 5-9, D-10098 Berlin (Germany); Choe, Hui-Woog, E-mail: kph@charite.de [Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Ziegelstrasse 5-9, D-10098 Berlin (Germany); Department of Chemistry, College of Natural Science, Chonbuk National University, 561-756 Chonju (Korea, Republic of)

    2005-05-01

    The expression, purification, crystallization and preliminary X-ray diffraction studies of mouse centrin1 are reported. Centrins belong to a family of Ca{sup 2+}-binding EF-hand proteins that play a fundamental role in centrosome duplication and the function of cilia. To shed light on the structure–function relationship of these proteins, mouse centrin1 has been crystallized. The mouse centrin1 has been expressed in Escherichia coli as a GST-centrin fusion protein containing a thrombin protease cleavage site between the fusion partners. Two constructs with different linking-sequence lengths were expressed and purified. Thrombin cleavage yielded functional centrin1 and N-terminally extended centrin1 containing 25 additional residues upstream of its N-terminus. Only N-terminally extended centrin1 (MW ≃ 22 240 Da) could be crystallized at room temperature, using 20–25%(w/v) PEG 1500, 5–10%(v/v) ethylene glycol and 1–2%(v/v) dioxane. Crystals were suitable for X-ray analysis, diffracting to 2.9 Å at 295 K using a rotating-anode X-ray source. They belong to space group C2, with unit-cell parameters a = 60.7, b = 59.6, c = 58.3 Å, β = 109.4°. Assuming the asymmetric cell to be occupied by one centrin1 molecule of 22.2 kDa, the unit cell contains 45% solvent with a crystal volume per protein weight, V{sub M}, of 2.2 Å{sup 3} Da{sup −1}.

  9. Cascaded-systems analysis of sandwich x-ray detectors

    Science.gov (United States)

    Kim, D. W.; Kim, J.; Yun, S.; Youn, H.; Kim, H. K.

    2016-12-01

    Active sandwich-like multilayer detectors have been developed, and their potential for motion-artifact-free dual-energy x-ray imaging at a single exposure has been demonstrated in the material decomposition context. Since the sandwich detector uses the x-ray beam transmittance through the front layer, direct x-ray interaction within photodiodes in the front layer is unavoidable, and which can increase noise in the front detector images. Similar direct x-ray interaction can also occur in the rear detector layer. To obtain a better contrast performance, an additional filter layer can be placed between the two detector layers. However, this filter layer can increase adversely noise in images obtained from the rear detector layer by reducing the number of x-ray photons reaching it. A theoretical model, which can describe the signal-to-noise performance of the sandwich detector as functions of various design parameters, has been developed by using a linear cascaded-systems theory. From the cascaded-systems analysis, the direct x-ray interaction increases noise at the high spatial frequencies where the number of secondary quanta lessens. The intermediate filter layer enhances the contribution of additive electronic noise in the overall noise performance of the rear detector layer. The detailed cascaded-systems analysis on the x-ray sandwich detectors are reported in comparisons with the measured noise-power spectra and detective quantum efficiencies. The developed model will be useful for a better design and practical use of a sandwich detector for single-shot dual-energy imaging.

  10. Study of crystal structure at high temperature phase in KIO sub 3 crystal by synchrotron powder X-ray diffraction

    CERN Document Server

    Kasatani, H; Kuroiwa, Y; Yagi, K; Katayama, R; Terauchi, H

    2003-01-01

    The accurate crystal structure of the I-phase in KIO sub 3 crystal has been obtained at 530 K, for the first time, by the MEM/Rietveld analysis from high-energy X-ray powder-diffraction data. The crystal structure of the I-phase is the rhombohedral perovskite structure (space group R3m; Z=1). The MEM charge-density distributions reveal that the shorter I-O bond exhibits a covalent bonding character and others (I-K, K-O and longer I-O bonds) an ionic.

  11. Analysis of the x-ray diffraction, etching, luminescence, photoconductivity, thermal and dielectric properties of an ADP crystal influenced by the bimetallic additive sodium metasilicate (Na2SiO3)

    Science.gov (United States)

    Anis, Mohd; Hussaini, S. S.; Shirsat, M. D.; Shaikh, R. N.; Muley, G. G.

    2016-10-01

    The present communication is focused on an investigation of the structural, optical, electrical and thermal properties of a sodium metasilicate (SMS)-doped ammonium dihydrogen phosphate (ADP) crystal. The slow evaporation solution technique has been adopted to grow the crystal with an optimum size of (10 × 6 × 4) mm3. The powder x-ray diffraction (PXRD) technique has been employed to confirm the crystalline nature, crystal structure and cell parameters of the crystal (a = b = 7.53 (±0.01) Ǻ, c = 7.59 (±0.03) Ǻ). The color-centered photoluminescence nature of the SMS-doped ADP crystal has been examined in the visible region of interest at an emission wavelength of 375 nm. Its frequency-dependent dielectric response has been investigated with reference to a pure ADP crystal to explore optoelectronic device applications. The thermal stability of the crystal has been examined by means of simultaneous thermogravimetric and differential thermal analysis, and its surface quality has been investigated by means of etching studies. Finally, photoconductivity studies have been employed to determine the nature of photoconductivity in the crystal.

  12. Novel zinc(II) and copper(II) complexes of a Mannich base derived from lawsone: Synthesis, single crystal X-ray analysis, ab initio density functional theory calculations and vibrational analysis.

    Science.gov (United States)

    Neves, Amanda P; Vargas, Maria D; Téllez Soto, Claudio A; Ramos, Joanna M; Visentin, Lorenzo do C; Pinheiro, Carlos B; Mangrich, Antônio S; de Rezende, Edivaltrys I P

    2012-08-01

    Zinc(II) and copper(II) complexes of a tridentate Mannich base L1 derived from 2-hydroxy-1,4-naphthoquinone, pyridinecarboxyaldehyde and 2-aminomethylpyridine, [ZnL1Cl(2)]·H(2)O 1 and [CuL1Cl(2)]·2H(2)O 2, have been synthesized and fully characterized. The structure of complex 1 has been elucidated by a single crystal X-ray diffraction study: the zinc atom is pentacoordinate and the coordination geometry is a distorted square base pyramid, with a geometric structural parameter τ equal to 0.149. Vibrational spectroscopy and ab initio DFT calculations of both compounds have confirmed that the two complexes exhibit similar structures. Full assignment of the vibrational spectra was also supported by careful analysis of the distorted geometries generated by the normal modes. Copyright © 2012 Elsevier B.V. All rights reserved.

  13. Instrumentation and data analysis for hard X ray astronomy

    Science.gov (United States)

    Zhang, Shuang Nan

    The current status of hard x ray astronomy is reviewed. The applicability of various hard x ray detectors in such new telescopes are discussed and the current status of hard x ray telescope design is reviewed. Background production mechanisms in hard x ray telescopes are discussed and some techniques for background reduction are also discussed. A simple method for estimating the optimum detector thickness is presented and the use of some detector materials which should minimize the neutron background is proposed. Three imaging techniques are briefly described. A simple discussion about their relative merits has suggested that the rotating modulation collimator (RMC) technique based on an improved detector technique provides the best imaging system. The pulse shape discrimination (PSD) technique is essential for the realization of such new detectors. The basic principles of various PSD methods are made for hard x ray phoswich detector applications. A new fast-veto technique is proposed and may be used in a quadruple phoswich detector system to provide good energy resolution and efficient background rejection. A proposed satellite-borne hard x ray telescope (CHIXSAT), which would use such detectors as its main detection elements, is described. A range of statistical data analysis methods for hard x ray and gamma ray astronomy are studied. Fisher's fact test is found to give the most reliable significance test. Methods for parameter estimation, including upper limit calculations, are described. The sensitivity of a telescope is defined with clear statistical meaning and a method for estimating the sensitivity is derived. A new method, called the chi3-test is proposed to be unbiased and have a very high power for multiple on-off observations, especially in searching for transient sources.

  14. Quantitative analysis by synchrotron radiation induced X-ray fluorescence at lure

    Science.gov (United States)

    Chevallier, P.; Brissaud, I.; Wang, J. X.

    1990-04-01

    The main features that makes synchrotron radiation an ideal source for X-ray fluorescence analysis are emphasized. Examples of quantitative analysis are given and a new type of spectrometer taking advantage of the focusing properties of a flat mosaic crystal and a position sensitive detector is described.

  15. Microspectroscopic soft X-ray analysis of keratin based biofibers.

    Science.gov (United States)

    Späth, Andreas; Meyer, Markus; Semmler, Sonja; Fink, Rainer H

    2015-03-01

    Scanning soft X-ray transmission microspectroscopy (STXM) and transmission electron microscopy (TEM) have been employed for a high-resolution morphological and chemical analysis of hair fibers from human, sheep and alpaca. STXM allows optimum contrast imaging of the main hair building blocks due to tuneable photon energy. Chemical similarities and deviations for the human hair building blocks as well as for the three investigated species are discussed on the basis of the local near-edge X-ray absorption fine structure (NEXAFS). The spectra of melanosomes corroborate the state-of-the-art model for the chemical structure of eumelanin. Complementary TEM micrographs reveal the occurrence of cortex sectioning in alpaca hair to some extent. A spectroscopic analysis for human hair cortex indicates low mass loss upon soft X-ray irradiation, but transformation of chemical species with decreasing amount of peptide bonds and increasing NEXAFS signal for unsaturated carbon-carbon bonds.

  16. Energy dispersive X-ray analysis in the electron microscope

    CERN Document Server

    Bell, DC

    2003-01-01

    This book provides an in-depth description of x-ray microanalysis in the electron microscope. It is sufficiently detailed to ensure that novices will understand the nuances of high-quality EDX analysis. Includes information about hardware design as well as the physics of x-ray generation, absorption and detection, and most post-detection data processing. Details on electron optics and electron probe formation allow the novice to make sensible adjustments to the electron microscope in order to set up a system which optimises analysis. It also helps the reader determine which microanalytical me

  17. Nuclear fusion induced by X-rays in a crystal

    CERN Document Server

    Belyaev, V B; Otto, J; Rakityansky, S A

    2016-01-01

    The nuclei that constitute a crystalline lattice, oscillate relative to each other with a very low energy that is not sufficient to penetrate through the Coulomb barriers separating them. An additional energy, which is needed to tunnel through the barrier and fuse, can be supplied by external electromagnetic waves (X-rays or the synchrotron radiation). Exposing to the X-rays the solid compound LiD (lithium-deuteride) for the duration of 111 hours, we have detected 88 events of the nuclear fusion d+Li6 ---> Be8*. Our theoretical estimate agrees with what we observed. One of possible applications of the phenomenon we found, could be the measurements of the rates of various nuclear reactions (not necessarily fusion) at extremely low energies inaccessible in accelerator experiments.

  18. Preliminary results of absolute wavelength calibration of imaging X-ray crystal spectrometer on EAST

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Xiayun [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031 (China); University of Science and Technology of China, Hefei 230026 (China); Wang, Fudi [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031 (China); Chen, Jun [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031 (China); University of Science and Technology of China, Hefei 230026 (China); Lyu, Bo, E-mail: blu@ipp.ac.cn [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031 (China); Li, Yingying; Fu, Jia; Xu, Liqing [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031 (China); Shi, Yuejiang [University of Science and Technology of China, Hefei 230026 (China); Department of Nuclear Engineering, Seoul National University, Seoul 151-742 (Korea, Republic of); Ye, Minyou [University of Science and Technology of China, Hefei 230026 (China); Wan, Baonian [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031 (China)

    2015-10-15

    Highlights: • The absolute wavelength calibration method for X-ray crystal spectrometer using X-ray fluorescence of the appropriate materials was first tested on EAST, and the preliminary experimental results were obtained. • The experimental results were thoroughly discussed and suggestion for further improvements of the experimental arrangement was proposed. • Rotation calibration of X-ray crystal spectrometer on EAST using MHD frequency was presented when the absolute wavelength calibration method is unavailable currently. - Abstract: Imaging X-ray crystal spectrometers (XCS) are currently operating on several major tokamaks to provide profiles of ion temperature and rotation velocity. In order to acquire absolute rotation velocity, several indirect methods were pursued previously, however the direct and effective method is to use known X-ray lines for wavelength calibration. One way to produce standard spectral lines is X-ray fluorescence, which could be excited by X-rays from tokamak plasmas. As part of the upgrade of XCS system on EAST, wavelength calibration was studied using cadmium's L-shell lines, namely Lα{sub 1} line (3.9564 Å) and Lα{sub 2} line (3.9650 Å) as the reference wavelength. The Geant 4 code was used to optimize foil thickness to achieve a reasonable X-ray fluorescence intensity. The Cd foil was placed between the beryllium window and crystal and could be retracted to provide in situ wavelength calibration. The detailed arrangement and preliminary wavelength calibration results of imaging X-ray crystal spectrometer on EAST are presented, plus the calibration using MHD frequency.

  19. X-Ray Diffraction and Imaging Study of Imperfections of Crystallized Lysozyme with Coherent X-Rays

    Science.gov (United States)

    Hu, Zheng-Wei; Chu, Y. S.; Lai, B.; Cai, Z.; Thomas, B. R.; Chernov, A. A.

    2003-01-01

    Phase-sensitive x-ray diffraction imaging and high angular-resolution diffraction combined with phase contrast radiographic imaging are employed to characterize defects and perfection of a uniformly grown tetragonal lysozyme crystal in symmetric Laue case. The fill width at half-maximum (FWHM) of a 4 4 0 rocking curve measured from the original crystal is approximately 16.7 arcseconds, and defects, which include point defects, line defects, and microscopic domains, have been clearly observed in the diffraction images of the crystal. The observed line defects carry distinct dislocation features running approximately along the growth front, and they have been found to originate mostly at a central growth area and occasionally at outer growth regions. Individual point defects trapped at a crystal nucleus are resolved in the images of high sensitivity to defects. Slow dehydration has led to the broadening of the 4 4 0 rocking curve by a factor of approximately 2.4. A significant change of the defect structure and configuration with drying has been revealed, which suggests the dehydration induced migration and evolution of dislocations and lattice rearrangements to reduce overall strain energy. The sufficient details of the observed defects shed light upon perfection, nucleation and growth, and properties of protein crystals.

  20. X-ray Peltier cooled detectors for X-ray fluorescence analysis

    Energy Technology Data Exchange (ETDEWEB)

    Loupilov, A. E-mail: bsi@bsi.lv; Sokolov, A.; Gostilo, V

    2001-06-01

    The recent results on development of X-ray Si(Li), Si-planar and CdTe p-i-n detectors cooled by Peltier coolers for fabrication of laboratory and portable XRF analysers for different applications are discussed. Low detection limits of XRF analysers are provided by increasing of detectors sensitive surface; improvement of their spectrometrical characteristics; decreasing of front-end-electronics noise level; Peltier coolers and vacuum chambers cooling modes optimization. Solution of all mentioned tasks allowed to develop Peltier cooled detectors with the following performances: (1.) Si(Li) detectors: S=20 mm{sup 2}, thickness=3.5 mm, 175 eV (5.9 keV), 430 eV (59.6 keV); S=100 mm{sup 2}; thickness=4.5 mm, 270 eV (5.9 keV), 485 eV (59.6 keV). (2.) Si-planar detector: S=10 mm{sup 2}, thickness=0.4 mm, 230 eV (5.9 keV), 460 eV (59.6 keV). (3.) CdTe p-i-n detectors: S=16 mm{sup 2}, thickness=0.5 mm, 350 eV (5.9 keV), 585 eV (59.6 keV). S=16 mm{sup 2}, thickness=1.2 mm, 310 eV (5.9 keV), 600 eV (59.6 keV). Advantages and disadvantages of all types of detectors for X-ray fluorescence analysis are compared. Spectra are presented. Application of different XRF analysers based on developed detectors in medicine, environmental science, industry, cryminalistics and history of art are demonstrated.

  1. The mannose-specific lectin domains of Flo1p from Saccharomyces cerevisiae and Lg-Flo1p from S. pastorianus: crystallization and preliminary X-ray diffraction analysis of the adhesin-carbohydrate complexes.

    Science.gov (United States)

    Ielasi, Francesco S; Goyal, Parveen; Sleutel, Mike; Wohlkonig, Alexandre; Willaert, Ronnie G

    2013-07-01

    Flo1p and Lg-Flo1p are two cell-wall adhesins belonging to the Flo (flocculation) protein family from the yeasts Saccharomyces cerevisiae and S. pastorianus. The main function of these modular proteins endowed with calcium-dependent lectin activity is to mediate cell-cell adhesion events during yeast flocculation, a process which is well known at the cellular level but still not fully characterized from a molecular perspective. Recently, structural features of the N-terminal Flo lectin domains, including the N-terminal domain of Lg-Flo1p (N-Lg-Flo1p), and their interactions with carbohydrate molecules have been investigated. However, structural data concerning the N-terminal domain of Flo1p (N-Flo1p), which is the most specific among the Flo proteins, are missing and information about the N-Lg-Flo1p-carbohydrate interaction still lacks detailed structural insight. Here, the crystallization and preliminary X-ray characterization of the apo form and the mannose complex of N-Flo1p and X-ray analysis of N-Lg-Flo1p crystals soaked in α-1,2-mannobiose are reported. The N-Flo1p crystals diffracted to a resolution of 1.43 Å in the case of the apo form and to 2.12 Å resolution for the mannose complex. Both crystals were orthorhombic and belonged to space group P212121, with one molecule in the asymmetric unit. The N-Lg-Flo1p-α-1,2-mannobiose complex crystal diffracted to 1.73 Å resolution and belonged to the monoclinic space group P1211 with two molecules in the asymmetric unit.

  2. Phase Sensitive X-Ray Diffraction Imaging of Defects in Biological Macromolecular Crystals

    Science.gov (United States)

    Hu, Z. W.; Lai, B.; Chu, Y. S.; Cai, Z.; Mancini, D. C.; Thomas, B. R.; Chernov, A. A.; Curreri, Peter A. (Technical Monitor)

    2002-01-01

    Characterization of defects and/or disorder in biological macromolecular crystals presents much greater challenges than in conventional small-molecule crystals. The lack of sufficient contrast of defects is often a limiting factor in x-ray diffraction topography of protein crystals. This has seriously hampered efforts to understand mechanisms and origins of formation of imperfections, and the role of defects as essential entities in the bulk of macromolecular crystals. In this report, we employ a phase sensitive x-ray diffraction imaging approach for augmenting the contrast of defects in protein crystals.

  3. Theoretical analysis on x-ray cylindrical grating interferometer

    CERN Document Server

    Cong, Wenxiang; Wang, Ge

    2015-01-01

    Grating interferometer is a state of art x-ray imaging approach, which can simultaneously acquire information of x-ray attenuation, phase shift, and small angle scattering. This approach is very sensitive to micro-structural variation and offers superior contrast resolution for biological soft tissues. The present grating interferometer often uses flat gratings, with serious limitations in the field of view and the flux of photons. The use of curved gratings allows perpendicular incidence of x-rays on the gratings, and gives higher visibility over a larger field of view than a conventional interferometer with flat gratings. In the study, we present a rigorous theoretical analysis of the self-imaging of curved transmission gratings based on Rayleigh-Sommerfeld diffraction. Numerical simulations have demonstrated the self-imaging phenomenon of cylindrical grating interferometer. The theoretical results are in agreement with the results of numerical simulations.

  4. Single-crystal diamond refractive lens for focusing X-rays in two dimensions

    Energy Technology Data Exchange (ETDEWEB)

    Antipov, S.; Baryshev, Sergey; Butler, J. E.; Antipova, O.; Liu, Zunping; Stoupin, S.

    2016-01-01

    The fabrication and performance evaluation of single-crystal diamond refractive X-ray lenses of which the surfaces are paraboloids of revolution for focusing X-rays in two dimensions simultaneously are reported. The lenses were manufactured using a femtosecond laser micromachining process and tested using X-ray synchrotron radiation. Such lenses were stacked together to form a standard compound refractive lens (CRL). Owing to the superior physical properties of the material, diamond CRLs could become indispensable wavefront-preserving primary focusing optics for X-ray free-electron lasers and the next-generation synchrotron storage rings. They can be used for highly efficient refocusing of the extremely bright X-ray sources for secondary optical schemes with limited aperture such as nanofocusing Fresnel zone plates and multilayer Laue lenses.

  5. Single-crystal diamond refractive lens for focusing X-rays in two dimensions.

    Science.gov (United States)

    Antipov, S; Baryshev, S V; Butler, J E; Antipova, O; Liu, Z; Stoupin, S

    2016-01-01

    The fabrication and performance evaluation of single-crystal diamond refractive X-ray lenses of which the surfaces are paraboloids of revolution for focusing X-rays in two dimensions simultaneously are reported. The lenses were manufactured using a femtosecond laser micromachining process and tested using X-ray synchrotron radiation. Such lenses were stacked together to form a standard compound refractive lens (CRL). Owing to the superior physical properties of the material, diamond CRLs could become indispensable wavefront-preserving primary focusing optics for X-ray free-electron lasers and the next-generation synchrotron storage rings. They can be used for highly efficient refocusing of the extremely bright X-ray sources for secondary optical schemes with limited aperture such as nanofocusing Fresnel zone plates and multilayer Laue lenses.

  6. Single Crystal Diamond Refractive Lens for Focusing X-rays in Two Dimensions

    CERN Document Server

    Antipov, S; Butler, J E; Antipova, O; Liu, Z; Stoupin, S

    2015-01-01

    We report the fabrication and performance evaluation of single crystal diamond refractive X-ray lenses with a paraboloid of rotation form factor for focusing X-rays in two dimensions simultaneously. The lenses were manufactured using a femtosecond laser micromachining process and tested using X-ray synchrotron radiation. Such lenses can be stacked together to form a traditional compound refractive lens (CRL). Due to the superior physical properties of the material, diamond CRLs are enabling and indispensable wavefront-preserving primary focusing optics for X-ray free-electron lasers and the next-generation synchrotron storage rings. They can be used for highly efficient refocusing of the extremely bright X-ray sources on secondary optical schemes with limited aperture such as nanofocusing Fresnel zone plates and multilayer Laue lenses.

  7. Domino Knoevenagel/Michael synthesis of 2,2'-arylmethylenebis(3- hydroxy-5,5-dimethyl-2-cyclohexen-1-one) derivatives catalyzed by silica-diphenic acid and their single crystal X-ray analysis

    Indian Academy of Sciences (India)

    RUPALI VAID; MONIKA GUPTA; RAJNI KANT; VIVEK K GUPTA

    2016-06-01

    An efficient and eco-friendly procedure has been developed for the synthesis of various 2,2'- arylmethylenebis(3-hydroxy-5,5-dimethyl-2-cyclohexene-1-one) derivatives which were isolated and characterizedby melting point, IR,$^{ 1}H-NMR$,$^{ 13}$C-NMR and mass spectrometric techniques. Out of the fourteencompounds synthesized, four compounds yielded crystals suitable for single crystal X-ray analysis whichshowed that 2,2'-phenylmethylenebis(3-hydroxy-5,5-dimethyl-2-cyclohexene-1-one) crystallizes in the tetragonalsystem with space group I41/a, 2,2’-(3-nitrophenyl)methylenebis(3-hydroxy-5,5-dimethyl-2-cyclohexene-1-one) crystallizes in the monoclinic system with space group P21/n, 2,2’-(4-nitrophenyl)methylenebis(3-hydroxy-5,5-dimethyl-2-cyclohexene-1-one) crystallizes in the orthorhombic system with space group Pca21and 2,2’-(4-chlorophenyl)methylenebis(3-hydroxy-5,5-dimethyl-2-cyclohexene-1-one) crystallizes in the monoclinicspace group P21/c.

  8. Spinal X-ray image analysis in scoliosis

    NARCIS (Netherlands)

    Sardjono, Tri Arief

    2007-01-01

    In this thesis new image analysis methods are discussed to determine the curvature of scoliotic patients characterised by the Cobb angle and to enhance the vertebral parts based on features from a frontal X-ray image. Chapter 1 provides some background information on scoliosis, how to diagnose it, t

  9. Extreme UV and X-ray scattering measurements from a rough LiF crystal surface characterized by electron micrography

    DEFF Research Database (Denmark)

    Alehyane; Arbaoui; Barchewitz

    1989-01-01

    XUV and X-ray scattering by a LiF crystal is measured. The angular distribution of the scattered radiation (ADSR) reveals characteristic features, side peaks or asymmetry. The surface of the sample is statistically characterized by a microdensitometer analysis of electron micrographs resolving th...

  10. Testing LaMgAl11O19 crystal for X-ray spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Chen, H; Beiersdorfer, P; Baronova, E; Kalashnikova, I; Stepanenko, M

    2004-03-31

    We investigated the properties of the rare earth crystal LaMgAl{sub 11}O{sub 19} and its application to soft X-ray spectroscopy. Its relative reflectivity and half width rocking curve were measured to up to the reflection order of 28. In addition, a comparative measurement of the iron L-shell soft X-ray line emission was made on the EBIT-I Livermore electron beam ion trap by fielding the LaMgAl{sub 11}O{sub 19} crystal side by side with a rubidium hydrogen phthalate crystal in a flat crystal spectrometer. From these measurements, reflectivity and spectral resolving power were determined.

  11. Evaluation of sagittal focusing for a spherical quartz crystal x-ray analyzer with synchrotron radiation

    Energy Technology Data Exchange (ETDEWEB)

    Pereira, Nino R.; Macrander, Albert T.; Hill, Kenneth W.; Baronova, Elena O.; George, Kevin M.; Kotick, Jordan T.

    2015-10-01

    To attain optimum performance in applications such as x-ray imaging and spectroscopy, a spherically bent crystal must diffract well across its entire surface. X-ray topography of sample crystals shows isolated regions where diffraction is problematic, even for a crystal where inspection with visible light does not suggest problems. Covering problem spots may improve the crystal’s focus and decrease the background. We explore the special properties of synchrotron radiation to examine typical spherical crystals from alpha-quartz, in a perpendicular geometry that is especially convenient to examine sagittal focusing.

  12. Numerical modeling of thermal loading of diamond crystal in X-ray FEL oscillators

    Science.gov (United States)

    Song, Mei-Qi; Zhang, Qing-Min; Guo, Yu-Hang; Li, Kai; Deng, Hai-Xiao

    2016-04-01

    Due to high reflectivity and high resolution of X-ray pulses, diamond is one of the most popular Bragg crystals serving as the reflecting mirror and mono-chromator in the next generation of free electron lasers (FELs). The energy deposition of X-rays will result in thermal heating, and thus lattice expansion of the diamond crystal, which may degrade the performance of X-ray FELs. In this paper, the thermal loading effect of diamond crystal for X-ray FEL oscillators has been systematically studied by combined simulation with Geant4 and ANSYS, and its dependence on the environmental temperature, crystal size, X-ray pulse repetition rate and pulse energy are presented. Our results show that taking the thermal loading effects into account, X-ray FEL oscillators are still robust and promising with an optimized design. Supported by National Natural Science Foundation of China (11175240, 11205234, 11322550) and Program for Changjiang Scholars and Innovative Research Team in University (IRT1280)

  13. Visualization of X-ray Beam Using CdWO4 Crystal for Macromolecular Crystallography

    Directory of Open Access Journals (Sweden)

    Kazimierz J. Gofron

    2011-12-01

    Full Text Available In synchrotron diffraction experiments, it is typically assumed that the X-ray beam at the sample position is uniform, stable and has dimensions that are controlled by the focus and slits settings. As might be expected, this process is much more complex. We present here an investigation of the properties of a synchrotron X-ray beam at the sample position. The X-ray beam is visualized with a single crystal scintillator that converts X-ray photons into visible light photons, which can be imaged using Structure Biology Center (SBC on-axis and off-axis microscope optics. The X-ray penetration is dependent on the composition of the scintillator (especially the effective Z, and X-ray energy. Several scintillators have been used to visualize X-ray beams. Here we compare CdWO4, PbWO4, Bi4Ge3O12, Y3Al5O12:Ce (YAG:Ce, and Gd2O2S:Tb (phosphor. We determined that scintillator crystals made of CdWO4 and similar high-Z materials are best suited for the energy range (7–20 keV and are most suitable for beam visualization for macromolecular crystallography applications. These scintillators show excellent absorption, optical, and mechanical properties.

  14. Visualization of X-ray Beam Using CdWO4 Crystal for Macromolecular Crystallography

    Directory of Open Access Journals (Sweden)

    Kazimierz J. Gofron

    2011-12-01

    Full Text Available In synchrotron diffraction experiments, it is typically assumed that the X-ray beam at the sample position is uniform, stable and has dimensions that are controlled by the focus and slits settings. As might be expected, this process is much more complex. We present here an investigation of the properties of a synchrotron X-ray beam at the sample position. The X-ray beam is visualized with a single crystal scintillator that converts X-ray photons into visible light photons, which can be imaged using Structure Biology Center (SBC on-axis and off-axis microscope optics. The X-ray penetration is dependent on the composition of the scintillator (especially the effective Z, and X-ray energy. Several scintillators have been used to visualize X-ray beams. Here we compare CdWO4, PbWO4, Bi4Ge3O12, Y3Al5O12:Ce (YAG:Ce, and Gd2O2S:Tb (phosphor. We determined that scintillator crystals made of CdWO4 and similar high-Z materials are best suited for the energy range (7–20 keV and are most suitable for beam visualization for macromolecular crystallography applications. These scintillators show excellent absorption, optical, and mechanical properties.

  15. X-ray diffraction, X-ray photoelectron spectra, crystal structure, and optical properties of centrosymmetric strontium borate Sr2B16O26.

    Science.gov (United States)

    Reshak, Ali Hussain; Auluck, S; Kityk, I V; Chen, Xuean

    2009-07-09

    We report results of X-ray diffraction (XRD) and valence band X- ray photoelectron (VB-XPS) spectra for strontium borate Sr(2)B(16)O(26). The X-ray structural analysis shows that the single crystals of Sr(2)B(16)O(26) crystallize in the monoclinic space group P2(1)/c with a = 8.408(1) A, b = 16.672(1) A, c = 13.901(2) A, beta = 106.33(1) degrees , and Z = 4. The crystal structure consists of a 3D network of the complex borate anion [B(16)O(20)O(12/2)](4-), formed by 12 BO(3) triangles and four BO(4) tetrahedra, which can be viewed as three linked [B(3)O(3)O(4/2)](-) triborate groups bonded to one pentaborate [B(5)O(6)O(4/2)](-) group and two BO(3) triangles. Using this structure, we have performed theoretical calculations using the all-electron full potential linearized augmented plane wave (FP-LAPW) method for the band structure, density of states, electron charge density, and the frequency-dependent optical properties. Our experimental VB-XPS of Sr(2)B(16)O(26) is compared with results of our FP-LAPW calculations. Our calculations show that the valence band maximum (VBM) and conduction band minimum (CBM) are located at Gamma of the Brillouin zone (BZ) resulting in a direct energy gap of about 5.31 eV. Our measured VB-XPS show reasonable agreement with our calculated total density of states for the valence band that is attributed to the use of the full potential method.

  16. Chemical Analysis of Reaction Rims on Olivine Crystals in Natural Samples of Black Dacite Using Energy-Dispersive X-Ray Spectroscopy, Lassen Peak, CA.

    Science.gov (United States)

    Graham, N. A.

    2014-12-01

    Lassen Volcanic Center is the southernmost volcanic region in the Cascade volcanic arc formed by the Cascadia Subduction Zone. Lassen Peak last erupted in 1915 in an arc related event producing a black dacite material containing xenocrystic olivine grains with apparent orthopyroxene reaction rims. The reaction rims on these olivine grains are believed to have formed by reactions that ensued from a mixing/mingling event that occurred prior to eruption between the admixed mafic andesitic magma and a silicic dacite host material. Natural samples of the 1915 black dacite from Lassen Peak, CA were prepared into 15 polished thin sections and carbon coated for analysis using a FEI Quanta 250 Scanning Electron Microscope (SEM) to identify and measure mineral textures and disequilibrium reaction rims. Observed mineralogical textures related to magma mixing include biotite and amphibole grains with apparent dehydration/breakdown rims, pyroxene-rimmed quartz grains, high concentration of microlites in glass matrix, and pyroxene/amphibole reaction rims on olivine grains. Olivine dissolution is evidenced as increased iron concentration toward convolute edges of olivine grains as observed by Backscatter Electron (BSE) imagery and elemental mapping using NSS spectral imaging software. In an attempt to quantify the area of reaction rim growth on olivine grains within these samples, high-resolution BSE images of 30 different olivine grains were collected along with Energy-Dispersive X-Ray Spectroscopy (EDS) of different phases. Olivine cores and rims were extracted from BSE images using Photoshop and saved as separate image files. ImageJ software was used to calculate the area (μm2) of the core and rim of these grains. Average pyroxene reaction rim width for 30 grains was determined to be 11.68+/-1.65 μm. Rim widths of all 30 grains were averaged together to produce an overall average rim width for the Lassen Peak black dacite. By quantifying the reaction rims on olivine grains

  17. Crystallization and preliminary X-ray analysis of the low-affinity complex between human leukocyte antigen-G (HLA-G) and leukocyte Ig-like receptor B2 (LILRB2).

    Science.gov (United States)

    Shiroishi, Mitsunori; Maenaka, Katsumi

    2009-01-01

    Human leukocyte antigen-G (HLA-G) is a nonclassical MHC class I (MHCI) molecule that is expressed mainly on placenta trophoblast cells. Leukocyte Ig-like receptor B2 (LILRB2) is a human inhibitory immune receptor that recognizes HLA-G with a higher affinity than any other MHCI although this interaction is only in the microM range. The interaction between HLA-G and LILRB2 seems to play a dominant role in the escape of the fetus from the maternal immune response. Here we report the crystallization and x-ray analysis of the LILRB2/HLA-G complex. The extracellular domains of HLA-G and LILRB2 were expressed in Escherichia coli, refolded and purified. The initial crystallization trials using novel PEG-based screening sets provided crystals of the LILRB2/HLA-G complex with 40-50% PEG400 as the precipitant. These crystals belong to space group P3(1)21 (a=b=81.4 A, c=186.7 A, gamma=120 degrees ). Dehydration of the crystals by soaking them in a solution containing a higher concentration of PEG400 dramatically improved the resolution and also the mosaicity.

  18. Perfectly Cold Crystals: What Happens When They Are X-rayed?

    Science.gov (United States)

    vanderWoerd, Mark; Ferree, Darren S.; Snell, Edward H.

    2003-01-01

    For many macromolecular crystals the cryo-preservation of these crystals during X-ray data collection is of crucial importance, particularly at synchrotron facilities where the crystals rapidly receive a high dose of radiation. A practical variable to ensure adequate preservation is the variation of the cryo-protectant present when the crystal is preserved. Our initial approach to study X-ray diffraction data quality as a function of cryo-protectant present when preserving a xylose isomerase crystal shows that the data quality can be tremendously improved by recipe adjustment. Guided by crystal mosaicity estimates, we optimized crystal growth conditions to obtain cryo-preserved xylose isomerase crystals that withstand a very high dose of X-rays, with only the smallest amount of radiation damage at ultra-high resolution (1.2Angstroms). The rate at which damage occurs allowed us to collect a series of complete data sets, which show how the data degradation proceeds over time. We are here presenting data for the xylose isomerase crystallization recipe improvement and our interpretation of the crystal degradation process during X-ray data collection.

  19. Coherent X-ray radiation excited by a diverging relativistic electron beam in a single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Blazhevich, S. V., E-mail: noskovbupk@mail.ru; Noskov, A. V. [Belgorod State National Research University (Russian Federation)

    2015-05-15

    We develop a dynamic theory of coherent X-rays generated in a single-crystal wafer by a diverging relativistic electron beam. The dependence of the spectral-angular density of coherent X-ray radiation on the angle of divergence is analyzed for the case when the angular spread can be described by the 2D Gaussian distribution. The theory constructed here makes it possible to analyze coherent radiation for an arbitrary angular distribution of electrons in the beam as well.

  20. A multi-cone x-ray imaging Bragg crystal spectrometer

    Science.gov (United States)

    Bitter, M.; Hill, K. W.; Gao, Lan; Efthimion, P. C.; Delgado-Apariccio, L.; Lazerson, S.; Pablant, N.

    2016-11-01

    This article describes a new x-ray imaging Bragg crystal spectrometer, which—in combination with a streak camera or a gated strip detector—can be used for time-resolved measurements of x-ray line spectra at the National Ignition Facility and other high power laser facilities. The main advantage of this instrument is that it produces perfect images of a point source for each wavelength in a selectable spectral range and that the detector plane can be perpendicular to the crystal surface or inclined by an arbitrary angle with respect to the crystal surface. These unique imaging properties are obtained by bending the x-ray diffracting crystal into a certain shape, which is generated by arranging multiple cones with different aperture angles on a common nodal line.

  1. Performance of the x-ray free-electron laser oscillator with crystal cavity

    Directory of Open Access Journals (Sweden)

    R. R. Lindberg

    2011-01-01

    Full Text Available Simulations of the x-ray free-electron laser (FEL oscillator are presented that include the frequency-dependent Bragg crystal reflectivity and the transverse diffraction and focusing using the two-dimensional FEL code GINGER. A review of the physics of Bragg crystal reflectors and the x-ray FEL oscillator is made, followed by a discussion of its numerical implementation in GINGER. The simulation results for a two-crystal cavity and realistic FEL parameters indicate ∼10^{9} photons in a nearly Fourier-limited, ps pulse. Compressing the electron beam to 100 A and 100 fs results in comparable x-ray characteristics for relaxed beam emittance, energy spread, and/or undulator parameters, albeit in a larger radiation bandwidth. Finally, preliminary simulation results indicate that the four-crystal FEL cavity can be tuned in energy over a range of a few percent.

  2. Time-Resolved Soft X-ray Diffraction Reveals Transient Structural Distortions of Ternary Liquid Crystals

    Directory of Open Access Journals (Sweden)

    Klaus Mann

    2009-11-01

    Full Text Available Home-based soft X-ray time-resolved scattering experiments with nanosecond time resolution (10 ns and nanometer spatial resolution were carried out at a table top soft X-ray plasma source (2.2–5.2 nm. The investigated system was the lyotropic liquid crystal C16E7/paraffin/glycerol/formamide/IR 5. Usually, major changes in physical, chemical, and/or optical properties of the sample occur as a result of structural changes and shrinking morphology. Here, these effects occur as a consequence of the energy absorption in the sample upon optical laser excitation in the IR regime. The liquid crystal shows changes in the structural response within few hundred nanoseconds showing a time decay of 182 ns. A decrease of the Bragg peak diffracted intensity of 30% and a coherent macroscopic movement of the Bragg reflection are found as a response to the optical pump. The Bragg reflection movement is established to be isotropic and diffusion controlled (1 μs. Structural processes are analyzed in the Patterson analysis framework of the time-varying diffraction peaks revealing that the inter-lamellar distance increases by 2.7 Å resulting in an elongation of the coherently expanding lamella crystallite. The present studies emphasize the possibility of applying TR-SXRD techniques for studying the mechanical dynamics of nanosystems.

  3. Time-resolved soft X-ray diffraction reveals transient structural distortions of ternary liquid crystals.

    Science.gov (United States)

    Quevedo, Wilson; Peth, Christian; Busse, Gerhard; Scholz, Mirko; Mann, Klaus; Techert, Simone

    2009-11-04

    Home-based soft X-ray time-resolved scattering experiments with nanosecond time resolution (10 ns) and nanometer spatial resolution were carried out at a table top soft X-ray plasma source (2.2-5.2 nm). The investigated system was the lyotropic liquid crystal C(16)E(7)/paraffin/glycerol/formamide/IR 5. Usually, major changes in physical, chemical, and/or optical properties of the sample occur as a result of structural changes and shrinking morphology. Here, these effects occur as a consequence of the energy absorption in the sample upon optical laser excitation in the IR regime. The liquid crystal shows changes in the structural response within few hundred nanoseconds showing a time decay of 182 ns. A decrease of the Bragg peak diffracted intensity of 30% and a coherent macroscopic movement of the Bragg reflection are found as a response to the optical pump. The Bragg reflection movement is established to be isotropic and diffusion controlled (1 micros). Structural processes are analyzed in the Patterson analysis framework of the time-varying diffraction peaks revealing that the inter-lamellar distance increases by 2.7 A resulting in an elongation of the coherently expanding lamella crystallite. The present studies emphasize the possibility of applying TR-SXRD techniques for studying the mechanical dynamics of nanosystems.

  4. Crystallization and preliminary X-ray analysis of birch-pollen allergen Bet v 1 in complex with a murine monoclonal IgG Fab' fragment

    DEFF Research Database (Denmark)

    Spangfort, M D; Mirza, Osman Asghar; Gajhede, M

    1999-01-01

    The human type I allergic response is characterized by the presence of allergen-specific serum immunoglobulin E (IgE). Allergen-mediated cross-linking of receptor-bound IgE on the surface of mast cells and circulating basophils triggers the release of mediators, resulting in the development of th......, with unit-cell parameters a = 91.65, b = 99.14, c = 108.90 A, alpha = 105.7, beta = 98.32, gamma = 97.62 degrees, and diffract to 2.9 A resolution when analyzed at 100 K using synchrotron-generated X--rays....

  5. Crystallization and preliminary X-ray diffraction study of porcine carboxypeptidase B

    Energy Technology Data Exchange (ETDEWEB)

    Akparov, V. Kh., E-mail: valery@akparov.ru [Scientific Center of Russian Federation Research Institute for Genetics and Selection of Industrial Microorganisms (Russian Federation); Timofeev, V. I., E-mail: inna@ns.crys.ras.ru; Kuranova, I. P., E-mail: tostars@mail.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2015-05-15

    Crystals of porcine pancreatic carboxypeptidase B have been grown in microgravity by the capillary counter-diffusion method through a gel layer. The X-ray diffraction study showed that the crystals belong to sp. gr. P4{sub 1}2{sub 1}2 and have the following unit-cell parameters: a = b = 79.58 Å, c = 100.51 Å; α = β = γ = 90.00°. The X-ray diffraction data set suitable for the determination of the three-dimensional structure at atomic resolution was collected from one of the grown crystals at the SPring 8 synchrotron facility to 0.98 Å resolution.

  6. Visualization of membrane protein crystals in lipid cubic phase using X-ray imaging

    Energy Technology Data Exchange (ETDEWEB)

    Warren, Anna J. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); Armour, Wes [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); Oxford e-Research Centre, 7 Keble Road, Oxford OX1 3QG (United Kingdom); Axford, Danny; Basham, Mark; Connolley, Thomas; Hall, David R. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); Horrell, Sam [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); University of Liverpool, Liverpool L69 3BX (United Kingdom); McAuley, Katherine E.; Mykhaylyk, Vitaliy; Wagner, Armin; Evans, Gwyndaf, E-mail: gwyndaf.evans@diamond.ac.uk [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom)

    2013-07-01

    A comparison of X-ray diffraction and radiographic techniques for the location and characterization of protein crystals is demonstrated on membrane protein crystals mounted within lipid cubic phase material. The focus in macromolecular crystallography is moving towards even more challenging target proteins that often crystallize on much smaller scales and are frequently mounted in opaque or highly refractive materials. It is therefore essential that X-ray beamline technology develops in parallel to accommodate such difficult samples. In this paper, the use of X-ray microradiography and microtomography is reported as a tool for crystal visualization, location and characterization on the macromolecular crystallography beamlines at the Diamond Light Source. The technique is particularly useful for microcrystals and for crystals mounted in opaque materials such as lipid cubic phase. X-ray diffraction raster scanning can be used in combination with radiography to allow informed decision-making at the beamline prior to diffraction data collection. It is demonstrated that the X-ray dose required for a full tomography measurement is similar to that for a diffraction grid-scan, but for sample location and shape estimation alone just a few radiographic projections may be required.

  7. Improving the energy resolution of bent crystal X-ray spectrometers with position-sensitive detectors.

    Science.gov (United States)

    Honkanen, Ari Pekka; Verbeni, Roberto; Simonelli, Laura; Moretti Sala, Marco; Al-Zein, Ali; Krisch, Michael; Monaco, Giulio; Huotari, Simo

    2014-07-01

    Wavelength-dispersive high-resolution X-ray spectrometers often employ elastically bent crystals for the wavelength analysis. In a preceding paper [Honkanen et al. (2014). J. Synchrotron Rad. 21, 104-110] a theory for quantifying the internal stress of a macroscopically large spherically curved analyser crystal was presented. Here the theory is applied to compensate for the corresponding decrease of the energy resolution. The technique is demonstrated with a Johann-type spectrometer using a spherically bent Si(660) analyser in near-backscattering geometry, where an improvement in the energy resolution from 1.0 eV down to 0.5 eV at 9.7 keV incident photon energy was observed.

  8. Simultaneous X-ray diffraction from multiple single crystals of macromolecules

    DEFF Research Database (Denmark)

    Paithankar, Karthik S.; Sørensen, Henning Osholm; Wright, Jonathan P.

    2011-01-01

    The potential in macromolecular crystallography for using multiple crystals to collect X-ray diffraction data simultaneously from assemblies of up to seven crystals is explored. The basic features of the algorithms used to extract data and their practical implementation are described. The procedu...

  9. Crystallization and preliminary X-ray analysis of the complex of the first von Willebrand type C domain bound to bone morphogenetic protein 2

    Energy Technology Data Exchange (ETDEWEB)

    Qiu, Li-yan; Zhang, Jin-li [Lehrstuhl für Physiologische Chemie II, Theodor-Boveri-Institut (Biozentrum) der Universität Würzburg, Am Hubland, D-97074 Würzburg (Germany); Kotzsch, Alexander [Lehrstuhl für Molekulare Pflanzenphysiologie und Biophysik, Julius-von-Sachs Institut der Universität Würzburg, Julius-von-Sachs Platz 2, D-97082 Würzburg (Germany); Sebald, Walter [Lehrstuhl für Physiologische Chemie II, Theodor-Boveri-Institut (Biozentrum) der Universität Würzburg, Am Hubland, D-97074 Würzburg (Germany); Rudolf-Virchow-Zentrum (DFG Forschungszentrum) der Universität Würzburg, Versbacher Strasse 9, D-97070 Würzburg (Germany); Mueller, Thomas D., E-mail: mueller@botanik.uni-wuerzburg.de [Lehrstuhl für Molekulare Pflanzenphysiologie und Biophysik, Julius-von-Sachs Institut der Universität Würzburg, Julius-von-Sachs Platz 2, D-97082 Würzburg (Germany); Rudolf-Virchow-Zentrum (DFG Forschungszentrum) der Universität Würzburg, Versbacher Strasse 9, D-97070 Würzburg (Germany); Lehrstuhl für Physiologische Chemie II, Theodor-Boveri-Institut (Biozentrum) der Universität Würzburg, Am Hubland, D-97074 Würzburg (Germany)

    2008-04-01

    Crystals of the complex of the first von Willebrand type C domain (VWC1) of crossveinless 2 (CV2) bound to bone morphogenetic protein 2 (BMP2) exist in two tetragonal crystal forms belonging to either space group P4{sub 1}2{sub 1}2 or I4{sub 1}, with one complete BMP2 dimer and two CV2 VWC1 domains per asymmetric unit, and diffract to 2.6 Å resolution. Crossveinless 2 (CV2) is a member of the chordin family, a protein superfamily that modulates the activity of bone morphogenetic proteins such as BMP2. The BMPs represent a large group of secreted proteins that control many steps during embryonal development and in tissue and organ homeostasis in the adult organism. The gene encoding the first von Willebrand type C domain (VWC1) of CV2 was cloned, expressed in Escherichia coli and purified to homogeneity. The binary complex of CV2 VWC1 and BMP2 was purified and subjected to crystallization. Crystals of SeMet-labelled proteins were obtained in two different forms belonging to the tetragonal space groups P4{sub 1}2{sub 1}2 and I4{sub 1}, with unit-cell parameters a = b = 86.7, c = 139.2 Å and a = b = 83.7, c = 139.6 Å, respectively. Initial analysis suggests that a complete binary complex consisting of one BMP2 dimer bound to two CV2 VWC1 domains is present in the asymmetric unit.

  10. Self-standing quasi-mosaic crystals for focusing hard X-rays

    Energy Technology Data Exchange (ETDEWEB)

    Camattari, Riccardo; Guidi, Vincenzo; Bellucci, Valerio; Neri, Ilaria; Frontera, Filippo [Department of Physics and Earth Science, University of Ferrara, Via Saragat 1/c, 44122 Ferrara (Italy); CNR-IDASC SENSOR Lab. (Italy); Jentschel, Michael [Institut Laue Langevin, F-38042 Grenoble Cedex (France)

    2013-05-15

    A quasi mosaic bent crystal for high-resolution diffraction of X and {gamma} rays has been realized. A net curvature was imprinted to the crystal thanks to a series of superficial grooves to keep the curvature without external devices. The crystal highlights very high diffraction efficiency due to quasi mosaic curvature. Quasi mosaic crystals of this kind are proposed for the realization of a high-resolution focusing Laue lens for hard X-rays.

  11. X-ray texture analysis of paper coating pigments and the correlation with chemical composition analysis

    Science.gov (United States)

    Roine, J.; Tenho, M.; Murtomaa, M.; Lehto, V.-P.; Kansanaho, R.

    2007-10-01

    The present research experiments the applicability of x-ray texture analysis in investigating the properties of paper coatings. The preferred orientations of kaolin, talc, ground calcium carbonate, and precipitated calcium carbonate particles used in four different paper coatings were determined qualitatively based on the measured crystal orientation data. The extent of the orientation, namely, the degree of the texture of each pigment, was characterized quantitatively using a single parameter. As a result, the effect of paper calendering is clearly seen as an increase on the degree of texture of the coating pigments. The effect of calendering on the preferred orientation of kaolin was also evident in an independent energy dispersive spectrometer analysis on micrometer scale and an electron spectroscopy for chemical analysis on nanometer scale. Thus, the present work proves x-ray texture analysis to be a potential research tool for characterizing the properties of paper coating layers.

  12. Diffraction crystal for sagittally focusing x-rays

    Science.gov (United States)

    Ice, Gene E.; Sparks, Jr., Cullie J.

    1984-01-01

    The invention is a new type of diffraction crystal designed for sagittally focusing photons of various energies. The invention is based on the discovery that such focusing is not obtainable with conventional crystals because of distortion resulting from anticlastic curvature. The new crystal comprises a monocrystalline base having a front face contoured for sagittally focusing photons and a back face provided with rigid, upstanding, stiffening ribs restricting anticlastic curvature. When mounted in a suitable bending device, the reflecting face of the crystal can be adjusted to focus photons having any one of a range of energies.

  13. Diffraction crystals for sagittally focusing x-rays

    Science.gov (United States)

    Ice, G.E.; Sparks, C.J. Jr.

    1982-06-07

    The invention is a new type of diffraction crystal designed for sagittally focusing photons of various energies. The invention is based on the discovery that such focusing is not obtainable with conventional crystals because of distortion resulting from anticlastic curvature. The new crystal comprises a monocrystalline base having a front face contoured for sagittally focusing photons and a back face provided with rigid, upstanding, stiffening ribs restricting anticlastic curvature. When mounted in a suitable bending device, the reflecting face of the crystal can be adjusted to focus photons having any one of a range of energies.

  14. Development of an X-ray fluorescence holographic measurement system for protein crystals

    Science.gov (United States)

    Sato-Tomita, Ayana; Shibayama, Naoya; Happo, Naohisa; Kimura, Koji; Okabe, Takahiro; Matsushita, Tomohiro; Park, Sam-Yong; Sasaki, Yuji C.; Hayashi, Kouichi

    2016-06-01

    Experimental procedure and setup for obtaining X-ray fluorescence hologram of crystalline metalloprotein samples are described. Human hemoglobin, an α2β2 tetrameric metalloprotein containing the Fe(II) heme active-site in each chain, was chosen for this study because of its wealth of crystallographic data. A cold gas flow system was introduced to reduce X-ray radiation damage of protein crystals that are usually fragile and susceptible to damage. A χ-stage was installed to rotate the sample while avoiding intersection between the X-ray beam and the sample loop or holder, which is needed for supporting fragile protein crystals. Huge hemoglobin crystals (with a maximum size of 8 × 6 × 3 mm3) were prepared and used to keep the footprint of the incident X-ray beam smaller than the sample size during the entire course of the measurement with the incident angle of 0°-70°. Under these experimental and data acquisition conditions, we achieved the first observation of the X-ray fluorescence hologram pattern from the protein crystals with minimal radiation damage, opening up a new and potential method for investigating the stereochemistry of the metal active-sites in biomacromolecules.

  15. Development of an X-ray fluorescence holographic measurement system for protein crystals

    Energy Technology Data Exchange (ETDEWEB)

    Sato-Tomita, Ayana, E-mail: ayana.sato@jichi.ac.jp, E-mail: shibayam@jichi.ac.jp, E-mail: hayashi.koichi@nitech.ac.jp; Shibayama, Naoya, E-mail: ayana.sato@jichi.ac.jp, E-mail: shibayam@jichi.ac.jp, E-mail: hayashi.koichi@nitech.ac.jp; Okabe, Takahiro [Division of Biophysics, Department of Physiology, Jichi Medical University, Yakushiji, Shimotsuke 329-0498 (Japan); Happo, Naohisa [Department of Computer and Network Engineering, Graduate School of Information Sciences, Hiroshima City University, Asa-Minami-Ku, Hiroshima 731-3194 (Japan); Kimura, Koji [Department of Physical Science and Engineering, Nagoya Institute of Technology, Gokiso, Showa, Nagoya 466-8555 (Japan); Matsushita, Tomohiro [Japan Synchrotron Radiation Research Institute (JASRI), SPring-8, Sayo, Hyogo 679-5198 (Japan); Park, Sam-Yong [Drug Design Laboratory, Department of Medical Life Science, Yokohama City University, Suehiro, Tsurumi, Yokohama 230-0045 (Japan); Sasaki, Yuji C. [Department of Advanced Material Science, Graduate School of Frontier Science, The University of Tokyo, Kashiwanoha, Kashiwa 277-8561 (Japan); Hayashi, Kouichi, E-mail: ayana.sato@jichi.ac.jp, E-mail: shibayam@jichi.ac.jp, E-mail: hayashi.koichi@nitech.ac.jp [Department of Physical Science and Engineering, Nagoya Institute of Technology, Gokiso, Showa, Nagoya 466-8555 (Japan); Frontier Research Institute for Materials Science, Nagoya Institute of Technology, Gokiso, Showa, Nagoya 466-8555 (Japan)

    2016-06-15

    Experimental procedure and setup for obtaining X-ray fluorescence hologram of crystalline metalloprotein samples are described. Human hemoglobin, an α{sub 2}β{sub 2} tetrameric metalloprotein containing the Fe(II) heme active-site in each chain, was chosen for this study because of its wealth of crystallographic data. A cold gas flow system was introduced to reduce X-ray radiation damage of protein crystals that are usually fragile and susceptible to damage. A χ-stage was installed to rotate the sample while avoiding intersection between the X-ray beam and the sample loop or holder, which is needed for supporting fragile protein crystals. Huge hemoglobin crystals (with a maximum size of 8 × 6 × 3 mm{sup 3}) were prepared and used to keep the footprint of the incident X-ray beam smaller than the sample size during the entire course of the measurement with the incident angle of 0°-70°. Under these experimental and data acquisition conditions, we achieved the first observation of the X-ray fluorescence hologram pattern from the protein crystals with minimal radiation damage, opening up a new and potential method for investigating the stereochemistry of the metal active-sites in biomacromolecules.

  16. Crystallization and identification of the glycosylated moieties of two isoforms of the main allergen Hev b 2 and preliminary X-ray analysis of two polymorphs of isoform II

    Energy Technology Data Exchange (ETDEWEB)

    Fuentes-Silva, D. [Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Cuidad Universitaria, Coyoacán, México, DF 04510 (Mexico); Mendoza-Hernández, G. [Facultad de Medicina, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Cuidad Universitaria, Coyoacán, México, DF 04510 (Mexico); Stojanoff, V. [Brookhaven National Laboratory, National Synchrotron Light Source, Upton, NY (United States); Palomares, L. A. [Instituto de Biotecnología, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Cuidad Universitaria, Coyoacán, México, DF 04510 (Mexico); Zenteno, E. [Facultad de Medicina, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Cuidad Universitaria, Coyoacán, México, DF 04510 (Mexico); Torres-Larios, A. [Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Cuidad Universitaria, Coyoacán, México, DF 04510 (Mexico); Rodríguez-Romero, A., E-mail: adela@servidor.unam.mx [Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Cuidad Universitaria, Coyoacán, México, DF 04510 (Mexico)

    2007-09-01

    Crystallization of important glycoenzymes involved in IgE-mediated latex allergy. Latex from Hevea brasiliensis contains several allergenic proteins that are involved in type I allergy. One of them is Hev b 2, which is a β-1,3-glucanase enzyme that exists in different isoforms with variable glycosylation content. Two glucanase isoforms were isolated from trees of the GV-42 clone by gel filtration, affinity and ion-exchange chromatography. Isoform I had a carbohydrate content of about 20%, with N-linked N-acetyl-glucosamine, N-acetyl-galactosamine, fucose and galactose residues as the main sugars, while isoform II showed 6% carbohydrate content constisting of N-acetyl-glucosamine, fucose, mannose and xylose. Both isoforms were crystallized by the hanging-drop vapour-diffusion method. Isoform I crystals were grown using 0.2 M trisodium citrate dihydrate, 0.1 M Na HEPES pH 7.5 and 20%(v/v) 2-propanol, but these crystals were not appropriate for data collection. Isoform II crystals were obtained under two conditions and X-ray diffraction data were collected from both. In the first condition (0.2 M trisodium citrate, 0.1 M sodium cacodylate pH 6.5, 30% 2-propanol), crystals belonging to the tetragonal space group P4{sub 1} with unit-cell parameters a = b = 150.17, c = 77.41 Å were obtained. In the second condition [0.2 M ammonium acetate, 0.1 M trisodium citrate dihydrate pH 5.6, 30%(w/v) polyethylene glycol 4000] the isoform II crystals belonged to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 85.08, b = 89.67, c = 101.80 Å, β = 113.6°. Preliminary analysis suggests that there are four molecules of isoform II in both asymmetric units.

  17. Double-slit dynamical diffraction of X-rays in ideal crystals (Laue case).

    Science.gov (United States)

    Balyan, Minas K

    2010-11-01

    The theoretical investigation of double-slit dynamical X-ray diffraction in ideal crystals shows that, on the exit surface of crystals, interference fringes similar to Young's fringes are formed. An expression for the period of the fringes was obtained. The visibility of the fringes depending on temporal and spatial coherent properties of the incident beam is studied. The polarization state of the incident beam also affects the visibility of the fringes, which in turn depends on the size of the slits. The deviation from Bragg's exact angle causes a shift of the fringes and can also affect the amplitude of the intensity. One of the parameters on which the visibility of the fringes depends is the source-crystal distance. The proposed scheme can be used as a Rayleigh X-ray interferometer. Use of the scheme as a Michelson X-ray stellar interferometer is also possible.

  18. Crystal optics for precision x-ray spectroscopy on highly charged ions—conception and proof

    Science.gov (United States)

    Beyer, H. F.; Gassner, T.; Trassinelli, M.; Heß, R.; Spillmann, U.; Banaś, D.; Blumenhagen, K.-H.; Bosch, F.; Brandau, C.; Chen, W.; Dimopoulou, Chr; Förster, E.; Grisenti, R. E.; Gumberidze, A.; Hagmann, S.; Hillenbrand, P.-M.; Indelicato, P.; Jagodzinski, P.; Kämpfer, T.; Kozhuharov, Chr; Lestinsky, M.; Liesen, D.; Litvinov, Yu A.; Loetzsch, R.; Manil, B.; Märtin, R.; Nolden, F.; Petridis, N.; Sanjari, M. S.; Schulze, K. S.; Schwemlein, M.; Simionovici, A.; Steck, M.; Stöhlker, Th; Szabo, C. I.; Trotsenko, S.; Uschmann, I.; Weber, G.; Wehrhan, O.; Winckler, N.; Winters, D. F. A.; Winters, N.; Ziegler, E.

    2015-07-01

    The experimental investigation of quantum-electrodydamic contributions to the binding energies of inner shells of highly charged heavy ions requires an accurate spectroscopy in the region of hard x-rays suitable at a limited source strength. For this purpose the focusing compensated asymmetric Laue crystal optics has been developed and a twin-spectrometer assembly has been built and commissioned at the experimental storage ring of the GSI Helmholtzzentrum Darmstadt. We characterize the crystal optics and demonstrate the usefulness of the instrumentation for accurate spectroscopy of both stationary and fast moving x-ray sources. The experimental procedures discussed here may also be applied for other spectroscopic studies where a transition from conventional germanium x-ray detectors to crystal spectrometers seems too demanding because of low source intensity.

  19. Batch crystallization of rhodopsin for structural dynamics using an X-ray free-electron laser

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Wenting; Nogly, Przemyslaw; Rheinberger, Jan; Kick, Leonhard M.; Gati, Cornelius; Nelson, Garrett; Deupi, Xavier; Standfuss, Jörg; Schertler, Gebhard; Panneels, Valérie, E-mail: valerie.panneels@psi.ch [Paul Scherrer Institute, OFLC/103, 5232 Villigen-PSI (Switzerland)

    2015-06-27

    A new batch preparation method is presented for high-density micrometre-sized crystals of the G protein-coupled receptor rhodopsin for use in time-resolved serial femtosecond crystallography at an X-ray free-electron laser using a liquid jet. Rhodopsin is a membrane protein from the G protein-coupled receptor family. Together with its ligand retinal, it forms the visual pigment responsible for night vision. In order to perform ultrafast dynamics studies, a time-resolved serial femtosecond crystallography method is required owing to the nonreversible activation of rhodopsin. In such an approach, microcrystals in suspension are delivered into the X-ray pulses of an X-ray free-electron laser (XFEL) after a precise photoactivation delay. Here, a millilitre batch production of high-density microcrystals was developed by four methodical conversion steps starting from known vapour-diffusion crystallization protocols: (i) screening the low-salt crystallization conditions preferred for serial crystallography by vapour diffusion, (ii) optimization of batch crystallization, (iii) testing the crystal size and quality using second-harmonic generation (SHG) imaging and X-ray powder diffraction and (iv) production of millilitres of rhodopsin crystal suspension in batches for serial crystallography tests; these crystals diffracted at an XFEL at the Linac Coherent Light Source using a liquid-jet setup.

  20. Analysis of sculptures using XRF and X-ray radiography

    Science.gov (United States)

    Calza, C.; Oliveira, D. F.; Freitas, R. P.; Rocha, H. S.; Nascimento, J. R.; Lopes, R. T.

    2015-11-01

    This work reports the analysis of two sacred images on polychrome wood using X-ray Radiography and Energy Dispersive X-Ray Fluorescence. The first case is the analysis of a sculpture portraying Saint Sebastian, the patron saint of Rio de Janeiro, which is considered the second most ancient sacred image of Brazil. This sculpture was made in Portugal and was transported to Brazil by Estácio Sá, founder of the city of Rio de Janeiro, in 1565. Nowadays, it is located on the main altar of the Church of Capuchin Friars. The second case is the analysis of a sculpture representing Our Lady of Conception, which is located in the D. João VI Museum (EBA/UFRJ, Rio de Janeiro). The objective of these analyses was to evaluate the general conditions of the sculptures, identifying possible problems and internal damages, areas that revealed signs of previous retouchings and the materials and pigments employed by the artists, in order to assist its restoration procedures. EDXRF measurements were carried out with a portable system, developed at the Nuclear Instrumentation Laboratory, consisting of a Si-PIN XR-100CR detector from Amptek and an Oxford TF3005 X-ray tube with W anode. An X-ray source, a CR System GE CR50P and IP detectors were used to perform the radiographs. The XRF analysis of the sculptures identified the original pigments in both cases and the radiographic images revealed details of the manufacture; restored regions; extensive use of lead white; presence of cracks on the wood; use of nails and spikes, etc.

  1. Complex assembly, crystallization and preliminary X-ray crystallographic analysis of the bovine CD8αα-BoLA-2*02201 complex.

    Science.gov (United States)

    Wang, Zhenbao; Chen, Rong; Tariq, Mansoor; Jiang, Bo; Chen, Zhaosan; Xia, Chun

    2014-06-01

    In order to clarify the structural characteristics of the bovine MHC class I molecule (BoLA-I) complexed with CD8αα (CD8αα-BoLA-I), bovine CD8αα, BoLA-I (BoLA-2*02201) and β2m were expressed and purified, and were then assembled with a peptide derived from Foot-and-mouth disease virus (FMDV-VP1YY9) and crystallized. The crystal diffracted to 1.7 Å resolution and belonged to space group P21, with unit-cell parameters a=53.9, b=103.8, c=61.8 Å, α=γ=90, β=96°. The asymmetric unit contained one complex, with a Matthews coefficient of 2.41 Å3 Da(-1) and a solvent content of 48.9%. The rotation-function Z-score and translation-function Z-score for molecular replacement were 3.4 and 8.9, respectively. In addition, SDS-PAGE analysis of CD8αα-BoLA-I crystals showed three bands corresponding to the molecular weights of BoLA-I heavy chain, β2m and CD8α. The structure of the CD8αα-BoLA-I complex should be helpful in obtaining insight into the interaction between bovine CD8αα and MHC class I molecules. Structure determination of BoLA-2*02201-FMDV-VP1YY9 will be useful in the design of vaccines for foot-and-mouth disease.

  2. Microbeam X-ray analysis in Poland - past and future

    Energy Technology Data Exchange (ETDEWEB)

    Kusinski, J, E-mail: kusinski@agh.edu.pl [AGH - University of Sciences and Technology, Faculty of Metals Engineering and Industrial Computer Science, Al. A. Mickiewicza 30, PL-30059 Krakow (Poland)

    2010-02-15

    The article provides an overview of the development of electron beam X-ray microanalysis (EPMA) in Poland. Since the introduction by Prof. Bojarski of EMPA over 45 years ago, tremendous advances in methodologies and in instrumentation have been made in order to improve the precision of quantitative compositional analysis, spatial resolution and analytical sensitivity. This was possible due to the activity of Applied Crystallography Committee at the Polish Academy of Sciences, as well as the groups of researches working in the Institute for Ferrous Metallurgy (Gliwice), the Technical University of Warsaw, the Silesian Technical University (Katowice), the AGH-University of Sciences and Technology (Krakow), and the Institute of Materials Science and Metallurgy Polish Academy of Sciences (Krakow). Based on the research examples realized by these teams, conferences, seminars and congresses organized, as well as books and academic textbooks issued, the evolution of electron beam X-ray microanalysis in Poland is demonstrated.

  3. Content analyses in GaMnAs by double-crystal X-ray diffraction

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    A model for analyzing point defects in compound crystals was improved. Based on this modified model,a method for measuring Mn content in GaMnAs was established. A technique for eliminating the zero-drift-error was also established in the experiments of X-ray diffraction. With these methods, the Mn content in GaMnAs single crystals fabricated by the ion-beam epitaxy system was analyzed.Kevwords: GaMnAs, diluted magnetic semiconductor, X-ray dff fraction, lattice parameter, content of Mn.

  4. Crystallization and Identification of the Glycosylated Moieties of Two Isoforms of the Main Allergen Hev b 2 and Preliminary X-ray Analysis of Two Polymorphs of Isoform ll

    Energy Technology Data Exchange (ETDEWEB)

    Fuentes-Silva,D.; Mendoza-Hernandez, G.; Stojanoff, V.; Palomares, L.; Zenteno, E.; Torres-Larios, A.; Rodriguez-Romero, A.

    2007-01-01

    Latex from Hevea brasiliensis contains several allergenic proteins that are involved in type I allergy. One of them is Hev b 2, which is a {beta}-1,3-glucanase enzyme that exists in different isoforms with variable glycosylation content. Two glucanase isoforms were isolated from trees of the GV-42 clone by gel filtration, affinity and ion-exchange chromatography. Isoform I had a carbohydrate content of about 20%, with N-linked N-acetyl-glucosamine, N-acetyl-galactosamine, fucose and galactose residues as the main sugars, while isoform II showed 6% carbohydrate content consisting of N-acetyl-glucosamine, fucose, mannose and xylose. Both isoforms were crystallized by the hanging-drop vapor-diffusion method. Isoform I crystals were grown using 0.2 M trisodium citrate dihydrate, 0.1 M Na HEPES pH 7.5 and 20%(v/v) 2-propanol, but these crystals were not appropriate for data collection. Isoform II crystals were obtained under two conditions and X-ray diffraction data were collected from both. In the first condition (0.2 M trisodium citrate, 0.1 M sodium cacodylate pH 6.5, 30% 2-propanol), crystals belonging to the tetragonal space group P4{sub 1} with unit-cell parameters a = b = 150.17, c = 77.41 {angstrom} were obtained. In the second condition [0.2 M ammonium acetate, 0.1 M trisodium citrate dihydrate pH 5.6, 30%(w/v) polyethylene glycol 4000] the isoform II crystals belonged to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 85.08, b = 89.67, c = 101.80 {angstrom}, {beta}= 113.6{sup o}. Preliminary analysis suggests that there are four molecules of isoform II in both asymmetric units.

  5. Crystallization and preliminary X-ray diffraction analysis of the Fab fragment of WO2, an antibody specific for the A[beta] peptides associated with Alzheimer's disease

    Energy Technology Data Exchange (ETDEWEB)

    Wun, Kwok S.; Miles, Luke A.; Crespi, Gabriela A.N.; Wycherley, Kaye; Ascher, David B.; Barnham, Kevin J.; Cappai, Roberto; Beyreuther, Konrad; Masters, Colin L.; Parker, Michael W.; McKinstry, William J. (SVIMR-A); (HeidelbergU); (WEHI); (Melbourne)

    2008-05-28

    The murine monoclonal antibody WO2 specifically binds the N-terminal region of the amyloid {beta} peptide (A{beta}) associated with Alzheimer's disease. This region of A{beta} has been shown to be the immunodominant B-cell epitope of the peptide and hence is considered to be a basis for the development of immunotherapeutic strategies against this prevalent cause of dementia. Structural studies have been undertaken in order to characterize the molecular basis for antibody recognition of this important epitope. Here, details of the crystallization and X-ray analysis of the Fab fragment of the unliganded WO2 antibody in two crystal forms and of the complexes that it forms with the truncated Az{beta} peptides A{beta}{sub 1-16} and A{beta}{sub 1-28} are presented. These crystals were all obtained using the hanging-drop vapour-diffusion method at 295 K. Crystals of WO2 Fab were grown in polyethylene glycol solutions containing ZnSO{sub 4}; they belonged to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1} and diffracted to 1.6 {angstrom} resolution. The complexes of WO2 Fab with either A{beta}{sub 1-16} or A{beta}{sub 1-28} were cocrystallized from polyethylene glycol solutions. These two complex crystals grew in the same space group, P2{sub 1}2{sub 1}2{sub 1}, and diffracted to 1.6 {angstrom} resolution. A second crystal form of WO2 Fab was grown in the presence of the sparingly soluble A{beta}{sub 1-42} in PEG 550 MME. This second form belonged to space group P2{sub 1} and diffracted to 1.9 {angstrom} resolution.

  6. Purification, crystallization and preliminary X-ray analysis of the galacto-N-biose-/lacto-N-biose I-binding protein (GL-BP) of the ABC transporter from Bifidobacterium longum JCM1217

    Energy Technology Data Exchange (ETDEWEB)

    Wada, Jun [Graduate School of Biostudies, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502 (Japan); Suzuki, Ryuichiro; Fushinobu, Shinya [Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 (Japan); Kitaoka, Motomitsu [National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642 (Japan); Wakagi, Takayoshi; Shoun, Hirofumi [Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 (Japan); Ashida, Hisashi [Graduate School of Biostudies, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502 (Japan); Kumagai, Hidehiko; Katayama, Takane, E-mail: takane@ishikawa-pu.ac.jp [Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836 (Japan); Yamamoto, Kenji [Graduate School of Biostudies, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502 (Japan)

    2007-09-01

    Preliminary X-ray analysis of the galacto-N-biose-/lacto-N-biose I-binding protein (GL-BP) of the ABC transporter from B. longum is described. A recombinant galacto-N-biose-/lacto-N-biose I-binding protein (GL-BP) from Bifidobacterium longum JCM1217 has been prepared and crystallized by the hanging-drop vapour-diffusion method using 10 mg ml{sup −1} purified enzyme, 0.01 M zinc sulfate, 0.1 M MES buffer pH 5.9–6.4 and 20–22%(v/v) PEG MME 550 in the presence of 5 mM disaccharide ligands. Suitable crystals grew after 10 d incubation at 293 K. The crystals belong to space group C222{sub 1}, with unit-cell parameters a = 106.3, b = 143.6, c = 114.6 Å for the lacto-N-biose I complex and a = 106.4, b = 143.4, c = 115.5 Å for the galacto-N-biose complex, and diffracted to 1.85 and 1.99 Å resolution, respectively.

  7. Sensitive X-ray detectors made of methylammonium lead tribromide perovskite single crystals

    Science.gov (United States)

    Wei, Haotong; Fang, Yanjun; Mulligan, Padhraic; Chuirazzi, William; Fang, Hong-Hua; Wang, Congcong; Ecker, Benjamin R.; Gao, Yongli; Loi, Maria Antonietta; Cao, Lei; Huang, Jinsong

    2016-05-01

    The large mobilities and carrier lifetimes of hybrid perovskite single crystals and the high atomic numbers of Pb, I and Br make them ideal for X-ray and gamma-ray detection. Here, we report a sensitive X-ray detector made of methylammonium lead bromide perovskite single crystals. A record-high mobility-lifetime product of 1.2 × 10-2 cm2 V-1 and an extremely small surface charge recombination velocity of 64 cm s-1 are realized by reducing the bulk defects and passivating surface traps. Single-crystal devices with a thickness of 2-3 mm show 16.4% detection efficiency at near zero bias under irradiation with continuum X-ray energy up to 50 keV. The lowest detectable X-ray dose rate is 0.5 μGyair s-1 with a sensitivity of 80 μC Gy-1air cm-2, which is four times higher than the sensitivity achieved with α-Se X-ray detectors. This allows the radiation dose applied to a human body to be reduced for many medical and security check applications.

  8. Synthesis, X-ray crystal structure and theoretical calculations of antileishmanial neolignan analogues

    Energy Technology Data Exchange (ETDEWEB)

    Nascimento, Josenaide P. do; Santos, Lourivaldo S.; Carmo, Maria Carolina L. do; Brasil, Davi S.B.; Alves, Claudio N., E-mail: nahum@ufpa.b [Universidade Federal do Para (UFPA), Belem, PA (Brazil). Inst. de Ciencias Exatas e Naturais; Santos, Regina Helena A.; Tozzo, Erica; Ferreira, Janaina G. [Universidade de Sao Paulo (IQSC/USP), Sao Carlos, SP (Brazil). Inst. de Quimica

    2010-07-01

    The synthesis and X-ray crystal diffraction structure of two analogues of neolignans, 2-(4-chlorophenyl)-1-phenylethanone (20) and 2-[(4-chlorophenyl)thio]-1-(3,4-dimethoxyphenyl) propan-1-one (12) is described. The compound 12 presents activity against intracellular Leishmania donovani and Leishmania amazonensis amastigotes that cause cutaneous and visceral leishmaniasis. In addition, the density functional theory (DFT) with the B3LYP hybrid functional was employed to calculate a set of molecular descriptors for nineteen synthetic analogues of neolignans with antileishmanial activities. Afterwards, the stepwise discriminant analysis was performed to investigate possible relationship between the molecular descriptors and biological activities. Through this analysis the compounds were classified into two groups active and inactive according to their degree of biological activities, and the more important properties were charges on some key atoms, electronic affinity and ClogP. (author)

  9. Crystal structure of defect-containing semiconductor nanocrystals. An X-ray diffraction study

    Energy Technology Data Exchange (ETDEWEB)

    Buljan, Maja [Karlova Univ., Prague (Czech Republic). Fakulta Matematicko-Fyzikalni; Institut Rudjer Boskovic, Zagreb (Croatia); Desnica, Uros V.; Radic, Nikola [Institut Rudjer Boskovic, Zagreb (Croatia); Drazic, Goran [Institut Jozef Stefan, Ljubljana (Slovenia); Matej, Zdenek; Vales, Vaclav; Holy, Vaclav [Karlova Univ., Prague (Czech Republic). Fakulta Matematicko-Fyzikalni

    2009-08-15

    Defects of crystal structure in semiconductor nanocrystals embedded in an amorphous matrix are studied by X-ray diffraction and a full-profile analysis of the diffraction curves based on the Debye formula. A new theoretical model is proposed, describing the diffraction from randomly distributed intrinsic and extrinsic stacking faults and twin blocks in the nanocrystals. The application of the model to full-profile analysis of experimental diffraction curves enables the determination of the concentrations of individual defect types in the nanocrystals. The method has been applied for the investigation of selforganized Ge nanocrystals in an SiO{sub 2} matrix, and the dependence of the structure quality of the nanocrystals on their deposition and annealing parameters was obtained. (orig.)

  10. First indirect x-ray imaging tests with an 88-mm diameter single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Lumpkin, A. H. [Fermilab; Macrander, A. T. [Argonne

    2017-02-01

    Using the 1-BM-C beamline at the Advanced Photon Source (APS), we have performed the initial indirect x - ray imaging point-spread-function (PSF) test of a unique 88-mm diameter YAG:Ce single crystal of only 100 - micron thickness. The crystal was bonded to a fiber optic plat e (FOP) for mechanical support and to allow the option for FO coupling to a large format camera. This configuration resolution was compared to that of self - supported 25-mm diameter crystals, with and without an Al reflective coating. An upstream monochromator was used to select 17-keV x-rays from the broadband APS bending magnet source of synchrotron radiation. The upstream , adjustable Mo collimators were then used to provide a series of x-ray source transverse sizes from 200 microns down to about 15-20 microns (FWHM) at the crystal surface. The emitted scintillator radiation was in this case lens coupled to the ANDOR Neo sCMOS camera, and the indirect x-ray images were processed offline by a MATLAB - based image processing program. Based on single Gaussian peak fits to the x-ray image projected profiles, we observed a 10.5 micron PSF. This sample thus exhibited superior spatial resolution to standard P43 polycrystalline phosphors of the same thickness which would have about a 100-micron PSF. Lastly, this single crystal resolution combined with the 88-mm diameter makes it a candidate to support future x-ray diffraction or wafer topography experiments.

  11. Secondary Extinction in Cylindrical and Spherical Crystals for X-Ray and Neutron Diffraction

    Institute of Scientific and Technical Information of China (English)

    胡华琛; 李兆桓; 杨斌; 沈彩万; 乔英

    2001-01-01

    The distribution of the reflection power ratio for a neutron or x-ray diffracted from a cylindrical crystal immersed in an homogenous incident beam is obtained by the numerical solution of the transfer equations for the first time. The profile well reflects all the physical properties of the absorption and extinction behaviour in the crystals. A systematic investigation of the secondary extinction for cylindrical and spherical crystals was carried out based on these results.

  12. Focusing characteristics of diamond crystal x-ray monochromators. An experimental and theoretical comparison

    DEFF Research Database (Denmark)

    Rio, M.S. del; Grübel, G.; Als-Nielsen, J.

    1995-01-01

    Perfect crystals in transmission (Laue) geometry can be used effectively for x-ray monochromators, and moreover, perfect Laue crystals show an interesting focusing effect when the incident beam is white and divergent. This focusing is directly dependent on the incident beam divergence and on the ...... from a diamond crystal in Lane geometry, and we analyze and explain the results by comparison with ray-tracing simulations. (C) 1995 American Institute of Physics....

  13. Controllable reflection of X-rays on crystals of saccharose

    CERN Document Server

    Navasardyan, M A; Hayrapetyan, K T; Gabrielyan, R T

    2003-01-01

    Multiple (ten times and more) increase in intensities of separate reflections and of lauegram reflections from organic single crystals of saccharose (C sub 1 2H sub 2 2O sub 1 1) was observed under influence of certain temperature gradient. On the base of the present experiment and the data of our previous woks we show that the controllable reflection process has a common nature and the intensity of the diffracted beam under external influences does not depend on the total number of electrons per unit volume of the unit cell of the single crystal.

  14. Crystallization and preliminary X-ray diffraction analysis of eukaryotic α2-macroglobulin family members modified by methylamine, proteases and glycosidases

    DEFF Research Database (Denmark)

    Goulas, T; Garcia-Ferrer, I; García-Piqué, S

    2014-01-01

    isolated native human α2M (hα2M) and its counterpart from chicken egg white (ovostatin) from natural sources. We developed specific purification protocols, and modified the purified proteins either by deglycosylation or by conversion to their induced forms. Native proteins yielded macroscopically...... disordered crystals or crystals only diffracting to very low resolution (>20 Å), respectively. Optimization of native hα2M crystals by varying chemical conditions was unsuccessful, while dehydration of native ovostatin crystals improved diffraction only slightly (10 Å). Moreover, treatment with several...

  15. Elliptically-bent crystal spectrograph for X-ray diagnosis of laser-produced plasmas

    Institute of Scientific and Technical Information of China (English)

    Xiancai Xiong(熊先才); Xianxin Zhong(钟先信); Shali Xiao(肖沙里); Guohong Yang(杨国洪); Jie Gao(高洁)

    2004-01-01

    In order to measure spatially and temporarily resolved laser-produced plasma X-ray spectra in 0.2 - 2nm region, a novel two-channel elliptically-bent crystal spectrograph has been developed. Dispersive elements are LiF, PET, Mica, and KAP crystals, which cover Bragg angles in the range of 30 - 67.5degrees. Eccentricity and focal distance of twin ellipses are 0.9586 and 1350 mm, respectively. Spatially resolved spectrum is photographically recorded with an X-ray film or X-CCD camera in one channel, and temporarily resolved one is photographically recorded with an X-ray streak camera in another channel,thus spatially and temporarily resolved spectra can be simultaneously obtained. Spectral images were acquired with X-CCD and PET in SHENGUANG-Ⅱ laser facility, and experimental results show that the spectral resolution of the spectrograph is about 0.002 nm.

  16. Measuring the X-ray Resolving Power of Bent Potassium Acid Phthalate Diffraction Crystals

    Energy Technology Data Exchange (ETDEWEB)

    Haugh, M. J. [NSTec; Wu, M. [SNL; Jacoby, K. D. [NSTec; Loisel, G. P. [SNL

    2014-11-01

    This report presents the results from measuring the X-ray resolving power of a curved potassium acid phthalate (KAP(001)) spectrometer crystal using two independent methods. It is part of a continuing effort to measure the fundamental diffraction properties of bent crystals that are used to study various characteristics of high temperature plasmas. Bent crystals like KAP(001) do not usually have the same diffraction properties as corresponding flat crystals. Models that do exist to calculate the effect of bending the crystal on the diffraction properties have simplifying assumptions and their accuracy limits have not been adequately determined. The type of crystals that we measured is being used in a spectrometer on the Z machine at Sandia National Laboratories (SNL) in Albuquerque, NM. The first technique for measuring the crystal resolving power measures the X-ray spectral line width of the characteristic lines from several metal anodes. The second method uses a diode X-ray source and a dual goniometer arrangement to measure the reflectivity curve of the KAP(001) crystal. The width of that curve is inversely proportional to the crystal resolving power. The measurement results are analyzed and discussed.

  17. The expression, purification, crystallization and preliminary X-ray analysis of a subcomplex of the peripheral stalk of ATP synthase from bovine mitochondria

    Energy Technology Data Exchange (ETDEWEB)

    Silvester, Jocelyn A.; Kane Dickson, Veronica; Runswick, Michael J. [The Medical Research Council Dunn Human Nutrition Unit, Hills Road, Cambridge CB2 2XY (United Kingdom); Leslie, Andrew G. W. [The Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH (United Kingdom); Walker, John E., E-mail: walker@mrc-dunn.cam.ac.uk [The Medical Research Council Dunn Human Nutrition Unit, Hills Road, Cambridge CB2 2XY (United Kingdom)

    2006-06-01

    A recombinant subcomplex of the peripheral stalk or stator domain of the ATP synthase from bovine mitochondria has been crystallized and a native data set has been collected to 2.8 Å resolution. A subcomplex of the peripheral stalk or stator domain of the ATP synthase from bovine mitochondria has been expressed to high levels in a soluble form in Escherichia coli. The subcomplex consists of residues 79–184 of subunit b, residues 1–124 of subunit d and the entire F{sub 6} subunit (76 residues). It has been purified and crystallized by vapour diffusion. The morphology and diffraction properties of the crystals of the subcomplex were improved by the presence of thioxane or 4-methylpyridine in the crystallization liquor. With a synchrotron-radiation source, these crystals diffracted to 2.8 Å resolution. They belong to the monoclinic space group P2{sub 1}.

  18. Crystallization and preliminary X-ray analysis of an anti-insect toxin BmK I6 from Buthus martensii Karsch scorpion

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    An excitatory anti-insect toxin from BmK scorpion, named BmK I6, has been purified and crystallized recently. Two crystal forms have been obtained by using ammonium sulfate as precipitant at different pH, one of which is single crystal. Diffraction data have been collected for the single crystal on a Mar Research 345 Image Plate. The analyses of the data show that the crystal can diffract to 0.28 nm resolution and belongs to the space group C2 with unit cell parameters a = 4.65 nm, b = 8.52 nm, c = 3.26 nm, α = γ = 90° ,β = 110.5° . There are 2 molecules per asymmetric unit according to its unit cell volume and molecular weight.

  19. Crystallization and X-ray diffraction analysis of the HMG domain of the chondrogenesis master regulator Sox9 in complex with a ChIP-Seq-identified DNA element

    Energy Technology Data Exchange (ETDEWEB)

    Vivekanandan, Saravanan; Moovarkumudalvan, Balasubramanian; Lescar, Julien; Kolatkar, Prasanna R.

    2015-10-30

    Sox9 is a fundamental sex-determining gene and the master regulator of chondrogenesis, and is involved in the development of various vital organs such as testes, kidney, heart and brain, and in skeletal development. Similar to other known Sox transcription factors, Sox9 recognizes and binds DNA with the consensus sequence C(T/A)TTG(T/A)(T/A) through the highly conserved HMG domain. Nonetheless, the molecular basis of the functional specificity of Sox9 in key developmental processes is still unclear. As an initial step towards a mechanistic understanding of Sox9 transcriptional regulation, the current work describes the details of the purification of the mouse Sox9 HMG domain (mSox9HMG), its crystallization in complex with a ChIP-Seq-identified FOXP2 promoter DNA element and the X-ray diffraction data analysis of this complex. The mSox9HMG–FOXP2 promoter DNA complex was crystallized by the hanging-drop vapour-diffusion method using 20% PEG 3350 in 200 mMsodium/potassium phosphate with 100 mMbis-tris propane at pH 8.5. The crystals diffracted to 2.7 Å resolution and the complex crystallized in the tetragonal space groupP41212, with unit-cell parametersa=b= 99.49,c= 45.89 Å. Crystal-packing parameters revealed that asymmetric unit contained one mSox9HMG–FOXP2 promoter DNA complex with an estimated solvent content of 64%.

  20. Crystallization and X-ray diffraction analysis of the HMG domain of the chondrogenesis master regulator Sox9 in complex with a ChIP-Seq-identified DNA element.

    Science.gov (United States)

    Vivekanandan, Saravanan; Moovarkumudalvan, Balasubramanian; Lescar, Julien; Kolatkar, Prasanna R

    2015-11-01

    Sox9 is a fundamental sex-determining gene and the master regulator of chondrogenesis, and is involved in the development of various vital organs such as testes, kidney, heart and brain, and in skeletal development. Similar to other known Sox transcription factors, Sox9 recognizes and binds DNA with the consensus sequence C(T/A)TTG(T/A)(T/A) through the highly conserved HMG domain. Nonetheless, the molecular basis of the functional specificity of Sox9 in key developmental processes is still unclear. As an initial step towards a mechanistic understanding of Sox9 transcriptional regulation, the current work describes the details of the purification of the mouse Sox9 HMG domain (mSox9HMG), its crystallization in complex with a ChIP-Seq-identified FOXP2 promoter DNA element and the X-ray diffraction data analysis of this complex. The mSox9HMG-FOXP2 promoter DNA complex was crystallized by the hanging-drop vapour-diffusion method using 20% PEG 3350 in 200 mM sodium/potassium phosphate with 100 mM bis-tris propane at pH 8.5. The crystals diffracted to 2.7 Å resolution and the complex crystallized in the tetragonal space group P41212, with unit-cell parameters a = b = 99.49, c = 45.89 Å. Crystal-packing parameters revealed that asymmetric unit contained one mSox9HMG-FOXP2 promoter DNA complex with an estimated solvent content of 64%.

  1. A von Hamos x-ray spectrometer based on a segmented-type diffraction crystal for single-shot x-ray emission spectroscopy and time-resolved resonant inelastic x-ray scattering studies.

    Science.gov (United States)

    Szlachetko, J; Nachtegaal, M; de Boni, E; Willimann, M; Safonova, O; Sa, J; Smolentsev, G; Szlachetko, M; van Bokhoven, J A; Dousse, J-Cl; Hoszowska, J; Kayser, Y; Jagodzinski, P; Bergamaschi, A; Schmitt, B; David, C; Lücke, A

    2012-10-01

    We report on the design and performance of a wavelength-dispersive type spectrometer based on the von Hamos geometry. The spectrometer is equipped with a segmented-type crystal for x-ray diffraction and provides an energy resolution in the order of 0.25 eV and 1 eV over an energy range of 8000 eV-9600 eV. The use of a segmented crystal results in a simple and straightforward crystal preparation that allows to preserve the spectrometer resolution and spectrometer efficiency. Application of the spectrometer for time-resolved resonant inelastic x-ray scattering and single-shot x-ray emission spectroscopy is demonstrated.

  2. Cryogenic cooling of x-ray crystals using porous matrix

    Energy Technology Data Exchange (ETDEWEB)

    Kuzay, T.M.

    1991-01-01

    It is well established that Si and SiC have very desirable thermophysical properties at cryogenic temperatures. This feature makes cryo-cooled optics potentially a good candidate for the first optical crystal of the presently built third generation synchrotron machines with very high heat flux levels. Currently, there is a great deal of interest in such cryo-cooled crystals pursued both experimentally and analytically. The analytical studies involve cut micro or capillary channel crystals. As opposed to the machined channels, porous matrices provide significant advantages. They operate very quietly. Such matrices are known to affect superior heat transfer enhancement. Data available in open literature suggest that surface heat flux levels up to {approximately}8 kW/cm{sup 2} are possible. For cryogens for which the boiling heat transfer heat flux is rather a low value in conventional geometries, the enhancement available with such matrices is a very significant characteristic. Cryogens are poor thermal conductors themselves. The fact that at the cryogenic temperatures the Si and/or SiC matrix itself becomes highly conductive, the matrix distributes the surface heat flux into the full volume effectively offsetting the poor conductivity of the coolant. In addition the tortuous path of the coolant through the matrix increases the dwell time for better heat transfer, however, at the expense of increased pressure drop. In this study, thermal conductivity of such composite matrices and the effective heat transfer coefficient obtainable using them are investigated. A first optics crystal model of Si with Si and/or Sic porous matrix as its heat exchanger and subject to prototype synchrotron level heat flux is analyzed and limits of the cooling possible with liquid nitrogen in single phase and subcooled boiling heat transfer modes are delineated.

  3. Purification, crystallization and preliminary X-ray analysis of a thermostable glycoside hydrolase family 43 β-xylosidase from Geobacillus thermoleovorans IT-08

    Energy Technology Data Exchange (ETDEWEB)

    Rohman, Ali [Department of Chemistry, Faculty of Mathematics and Natural Sciences, Airlangga University, Kampus C Unair, Jl. Mulyorejo, Surabaya 60115 (Indonesia); Oosterwijk, Niels van [Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen (Netherlands); Kralj, Slavko; Dijkhuizen, Lubbert [Laboratory of Microbial Physiology, University of Groningen, Kerklaan 30, 9750 NN Haren (Netherlands); Dijkstra, Bauke W. [Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen (Netherlands); Puspaningsih, Ni Nyoman Tri, E-mail: nyomantri@unair.ac.id [Department of Chemistry, Faculty of Mathematics and Natural Sciences, Airlangga University, Kampus C Unair, Jl. Mulyorejo, Surabaya 60115 (Indonesia)

    2007-11-01

    The β-xylosidase was crystallized using PEG 6000 as precipitant. 5% PEG 6000 yielded bipyramid-shaped tetragonal crystals diffracting to 1.55 Å resolution, and 13% PEG 6000 gave rectangular monoclinic crystals diffracting to 1.80 Å resolution. The main enzymes involved in xylan-backbone hydrolysis are endo-1,4-β-xylanase and β-xylosidase. β-Xylosidase converts the xylo-oligosaccharides produced by endo-1,4-β-xylanase into xylose monomers. The β-xylosidase from the thermophilic Geobacillus thermoleovorans IT-08, a member of glycoside hydrolase family 43, was crystallized at room temperature using the hanging-drop vapour-diffusion method. Two crystal forms were observed. Bipyramid-shaped crystals belonging to space group P4{sub 3}2{sub 1}2, with unit-cell parameters a = b = 62.53, c = 277.4 Å diffracted to 1.55 Å resolution. The rectangular crystals belonged to space group P2{sub 1}, with unit-cell parameters a = 57.94, b = 142.1, c = 153.9 Å, β = 90.5°, and diffracted to 1.80 Å resolution.

  4. Characterization of x-ray imaging crystal spectrometer for high-resolution spatially-resolved x-ray Thomson scattering measurements in shock-compressed experiments

    Science.gov (United States)

    Lu, J.; Hill, K. W.; Bitter, M.; Pablant, N. A.; Delgado-Aparicio, L. F.; Efthimion, P. C.; Lee, H. J.; Zastrau, U.

    2017-01-01

    We have proposed, designed and built a dual-channel x-ray imaging crystal spectrometer (XICS) for spectrally- and spatially-resolved x-ray Thomson scattering (XRTS) measurements in the Matter in Extreme Conditions (MEC) end station at the Linac Coherent Light Source (LCLS). This spectrometer employs two spherically-bent germanium (Ge) 220 crystals, which are combined to form a large aperture dispersive element with a spectral bandwidth of 300 eV that enables both the elastic and inelastic x-ray scattering peaks to be simultaneously measured. The apparatus and its characterization are described. A resolving power of 1900 was demonstrated and a spatial resolution of 12 μm was achieved in calibration tests. For XRTS measurements, a narrow-bandwidth (ΔE/Ecarbon plasma produced in shock-compressed samples of different forms of carbon. Preliminary results of the scattering experiments from Pyrolytic Graphite samples that illustrate the utility of the instrument are presented.

  5. Goniometer-based femtosecond X-ray diffraction of mutant 30S ribosomal subunit crystals

    Directory of Open Access Journals (Sweden)

    E. Han Dao

    2015-07-01

    Full Text Available In this work, we collected radiation-damage-free data from a set of cryo-cooled crystals for a novel 30S ribosomal subunit mutant using goniometer-based femtosecond crystallography. Crystal quality assessment for these samples was conducted at the X-ray Pump Probe end-station of the Linac Coherent Light Source (LCLS using recently introduced goniometer-based instrumentation. These 30S subunit crystals were genetically engineered to omit a 26-residue protein, Thx, which is present in the wild-type Thermus thermophilus 30S ribosomal subunit. We are primarily interested in elucidating the contribution of this ribosomal protein to the overall 30S subunit structure. To assess the viability of this study, femtosecond X-ray diffraction patterns from these crystals were recorded at the LCLS during a protein crystal screening beam time. During our data collection, we successfully observed diffraction from these difficult-to-grow 30S ribosomal subunit crystals. Most of our crystals were found to diffract to low resolution, while one crystal diffracted to 3.2 Å resolution. These data suggest the feasibility of pursuing high-resolution data collection as well as the need to improve sample preparation and handling in order to collect a complete radiation-damage-free data set using an X-ray Free Electron Laser.

  6. Crystallization and preliminary X-ray analysis of the subclass B3 metallo-β-lactamase SMB-1 that confers carbapenem resistance.

    Science.gov (United States)

    Wachino, Jun-ichi; Yamaguchi, Yoshihiro; Mori, Shigetarou; Yamagata, Yuriko; Arakawa, Yoshichika; Shibayama, Keigo

    2012-03-01

    The carbapenem-hydrolyzing subclass B3 metallo-β-lactamase SMB-1 was expressed in Escherichia coli and purified. Diffraction data were collected from two types of SMB-1 crystals that were obtained under different conditions. One crystal (SMB-1a) belonged to the trigonal space group P3(1) with unit-cell parameters a = b = 67.83, c = 48.67 Å, while the other crystal (SMB-1b) also belonged to space group P3(1) but with unit-cell parameters a = b = 67.25, c = 46.83 Å. Both crystals contained one molecule per asymmetric unit. Initial phases were determined by molecular replacement; further refinement and model building are in progress. © 2012 International Union of Crystallography

  7. Crystallization and preliminary X-ray diffraction of malate dehydrogenase from Plasmodium falciparum

    NARCIS (Netherlands)

    Wrenger, Carsten; Mueller, Ingrid B.; Butzloff, Sabine; Jordanova, Rositsa; Lunev, Sergey; Groves, Matthew R.

    2012-01-01

    The expression, purification, crystallization and preliminary X-ray diffraction characterization of malate dehydrogenase (MDH) from the malarial parasite Plasmodium falciparum (PfMDH) are reported. In order to gain a deeper understanding of the function and role of PfMDH, the protein was purified to

  8. X-RAY AND GAMMA-RAY LUMINESCENCE OF CE-3+ DOPED BAF2 CRYSTALS

    NARCIS (Netherlands)

    DORENBOS, P; VISSER, R; VANEIJK, CWE; HOLLANDER, RW; DENHARTOG, HW

    1991-01-01

    The scintillation properties of BaF2 doped with 0.002 to 10 mol% Ce3+ have been studied by means of X-ray and gamma ray excitation. The luminescence intensity increases with the Ce concentration until a maximum is reached for 0.2 mol% doped crystals. The light yield is then about 60% more intense th

  9. X-RAY AND GAMMA-RAY LUMINESCENCE OF CE-3+ DOPED BAF2 CRYSTALS

    NARCIS (Netherlands)

    DORENBOS, P; VISSER, R; VANEIJK, CWE; HOLLANDER, RW; DENHARTOG, HW

    1991-01-01

    The scintillation properties of BaF2 doped with 0.002 to 10 mol% Ce3+ have been studied by means of X-ray and gamma ray excitation. The luminescence intensity increases with the Ce concentration until a maximum is reached for 0.2 mol% doped crystals. The light yield is then about 60% more intense

  10. Doubly curved imaging Bragg crystal spectrometer for X-ray astronomy

    DEFF Research Database (Denmark)

    Byrnak, B. P.; Christensen, Finn Erland; Westergaard, Niels Jørgen Stenfeldt

    1985-01-01

    An X-ray spectrometer which is sensitive in the 0.5-7-keV energy range and is intended for use onboard astronomical satellites has been studied. The Bragg reflected rays from a doubly bent crystal positioned downstream of the focal plane of a grazing-incidence concentrator are focused along the a...

  11. Microcontroller-based servo for two-crystal X-ray monochromators.

    Science.gov (United States)

    Siddons, D P

    1998-05-01

    Microcontrollers have become increasingly easy to incorporate into instruments as the architectures and support tools have developed. The PIC series is particularly easy to use, and this paper describes a controller used to stabilize the output of a two-crystal X-ray monochromator at a given offset from its peak intensity position, as such monochromators are generally used.

  12. Characterization of calcium crystals in Abelia using x-ray diffraction and electron microscopes

    Science.gov (United States)

    Localization, chemical composition, and morphology of calcium crystals in leaves and stems of Abelia mosanensis and A. ×grandiflora were analyzed with a variable pressure scanning electron microscope (VP-SEM) equipped with an X-ray diffraction system, low temperature SEM (LT-SEM) and a transmission ...

  13. High spatial resolution X-ray and gamma ray imaging system using diffraction crystals

    Science.gov (United States)

    Smither, Robert K.

    2011-05-17

    A method and a device for high spatial resolution imaging of a plurality of sources of x-ray and gamma-ray radiation are provided. The device comprises a plurality of arrays, with each array comprising a plurality of elements comprising a first collimator, a diffracting crystal, a second collimator, and a detector.

  14. Crystallization and preliminary X-ray diffraction analysis of the periplasmic domain of the Escherichia coli aspartate receptor Tar and its complex with aspartate

    Energy Technology Data Exchange (ETDEWEB)

    Mise, Takeshi; Matsunami, Hideyuki; Samatey, Fadel A.; Maruyama, Ichiro N., E-mail: ichi@oist.jp [Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami, Okinawa 904-0495 (Japan)

    2014-08-27

    The periplasmic domain of the E. coli aspartate receptor Tar was cloned, expressed, purified and crystallized with and without bound ligand. The crystals obtained diffracted to resolutions of 1.58 and 1.95 Å, respectively. The cell-surface receptor Tar mediates bacterial chemotaxis toward an attractant, aspartate (Asp), and away from a repellent, Ni{sup 2+}. To understand the molecular mechanisms underlying the induction of Tar activity by its ligands, the Escherichia coli Tar periplasmic domain with and without bound aspartate (Asp-Tar and apo-Tar, respectively) were each crystallized in two different forms. Using ammonium sulfate as a precipitant, crystals of apo-Tar1 and Asp-Tar1 were grown and diffracted to resolutions of 2.10 and 2.40 Å, respectively. Alternatively, using sodium chloride as a precipitant, crystals of apo-Tar2 and Asp-Tar2 were grown and diffracted to resolutions of 1.95 and 1.58 Å, respectively. Crystals of apo-Tar1 and Asp-Tar1 adopted space group P4{sub 1}2{sub 1}2, while those of apo-Tar2 and Asp-Tar2 adopted space groups P2{sub 1}2{sub 1}2{sub 1} and C2, respectively.

  15. Cloning, expression, purification, crystallization and X-ray crystallographic analysis of CofB, the minor pilin subunit of CFA/III from human enterotoxigenic Escherichia coli.

    Science.gov (United States)

    Kawahara, Kazuki; Oki, Hiroya; Fukakusa, Shunsuke; Maruno, Takahiro; Kobayashi, Yuji; Motooka, Daisuke; Taniguchi, Tooru; Honda, Takeshi; Iida, Tetsuya; Nakamura, Shota; Ohkubo, Tadayasu

    2015-06-01

    Colonization factor antigen III (CFA/III) is one of the virulence factors of human enterotoxigenic Escherichia coli (ETEC) that forms the long, thin, proteinaceous fibres of type IV pili through assembly of its major and minor subunits CofA and CofB, respectively. The crystal structure of CofA has recently been reported; however, the lack of structural information for CofB, the largest among the known type IV pilin subunits, hampers a comprehensive understanding of CFA/III pili. In this study, constructs of wild-type CofB with an N-terminal truncation and the corresponding SeMet derivative were cloned, expressed, purified and crystallized. The crystals belonged to the rhombohedral space group R32, with unit-cell parameters a = b = 103.97, c = 364.57 Å for the wild-type construct and a = b = 103.47, c = 362.08 Å for the SeMet-derivatized form. Although the diffraction quality of these crystals was initially very poor, dehydration of the crystals substantially improved the resolution limit from ∼ 4.0 to ∼ 2.0 Å. The initial phase was solved by the single-wavelength anomalous dispersion (SAD) method using a dehydrated SeMet CofB crystal, which resulted in an interpretable electron-density map.

  16. Purification, crystallization and preliminary X-ray diffraction analysis of the carbohydrate-binding region of the Streptococcus gordonii adhesin GspB

    Energy Technology Data Exchange (ETDEWEB)

    Pyburn, Tasia M.; Yankovskaya, Victoria; Bensing, Barbara A.; Cecchini, Gary; Sullam, Paul M.; Iverson, T.M. (VA); (Vanderbilt); (UCSF)

    2012-07-11

    The carbohydrate-binding region of the bacterial adhesin GspB from Streptococcus gordonii strain M99 (GspB{sub BR}) was expressed in Escherichia coli and purified using affinity and size-exclusion chromatography. Separate sparse-matrix screening of GspB{sub BR} buffered in either 20 mM Tris pH 7.4 or 20 mM HEPES pH 7.5 resulted in different crystallographic behavior such that different precipitants, salts and additives supported crystallization of GspB{sub BR} in each buffer. While both sets of conditions supported crystal growth in space group P2{sub 1}2{sub 1}2{sub 1}, the crystals had distinct unit-cell parameters of a = 33.3, b = 86.7, c = 117.9 {angstrom} for crystal form 1 and a = 34.6, b = 98.3, c = 99.0 {angstrom} for crystal form 2. Additive screening improved the crystals grown in both conditions such that diffraction extended to beyond 2 {angstrom} resolution. A complete data set has been collected to 1.3 {angstrom} resolution with an overall R{sub merge} value of 0.04 and an R{sub merge} value of 0.33 in the highest resolution shell.

  17. X-Ray Diffraction and Fluorescence Instrument for Mineralogical Analysis at the Lunar Surface Project

    Data.gov (United States)

    National Aeronautics and Space Administration — We propose to develop LUNA, a compact and lightweight X-Ray Diffraction (XRD) / X-Ray Fluorescence (XRF) instrument for mineralogical analysis of regolith, rock...

  18. X-Ray Diffraction and Fluorescence Instrument for Mineralogical Analysis at the Lunar Surface Project

    Data.gov (United States)

    National Aeronautics and Space Administration — We propose to develop a compact and lightweight X-Ray Diffraction (XRD) / X-Ray Fluorescence (XRF) instrument for analysis of mineralogical composition of regolith,...

  19. Preparation, crystallization and preliminary X-ray diffraction analysis of the DNA-binding domain of the Ets transcription factor in complex with target DNA

    Energy Technology Data Exchange (ETDEWEB)

    Suwa, Yoshiaki; Nakamura, Teruya; Toma, Sachiko; Ikemizu, Shinji; Kai, Hirofumi; Yamagata, Yuriko, E-mail: yamagata@gpo.kumamoto-u.ac.jp [Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973 (Japan)

    2008-03-01

    The complex between the Ets domain of Ets2 and its target DNA has been crystallized. The crystals diffracted to 3.0 Å resolution. The Ets2 transcription factor is a member of the Ets transcription-factor family. Ets2 plays a role in the malignancy of cancer and in Down’s syndrome by regulating the transcription of various genes. The DNA-binding domain of Ets2 (Ets domain; ETSD), which contains residues that are highly conserved among Ets transcription-factor family members, was expressed as a GST-fusion protein. The aggregation of ETSD produced after thrombin cleavage could be prevented by treatment with NDSB-195 (nondetergent sulfobetaine 195). ETSD was crystallized in complex with DNA containing the Ets2 target sequence (GGAA) by the hanging-drop vapour-diffusion method. The best crystals were grown using 25% PEG 3350, 80 mM magnesium acetate, 50 mM sodium cacodylate pH 5.0/5.5 as the reservoir at 293 K. The crystals belonged to space group C2, with unit-cell parameters a = 85.89, b = 95.52, c = 71.89 Å, β = 101.7° and a V{sub M} value of 3.56 Å{sup 3} Da{sup −1}. Diffraction data were collected to a resolution of 3.0 Å.

  20. Crystallization and preliminary X-ray crystallographic analysis of adenosine 5′-monophosphate deaminase (AMPD) from Arabidopsis thaliana in complex with coformycin 5′-phosphate

    Energy Technology Data Exchange (ETDEWEB)

    Han, Byung Woo [Department of Biochemistry, University of Wisconsin-Madison, WI 53706-1544 (United States); Center for Eukaryotic Structural Genomics (CESG), University of Wisconsin-Madison, WI 53706-1549 (United States); Bingman, Craig A. [Center for Eukaryotic Structural Genomics (CESG), University of Wisconsin-Madison, WI 53706-1549 (United States); Mahnke, Donna K.; Sabina, Richard L. [Department of Biochemistry, The Medical College of Wisconsin, Milwaukee, WI 53226-4801 (United States); Phillips, George N. Jr, E-mail: phillips@biochem.wisc.edu [Department of Biochemistry, University of Wisconsin-Madison, WI 53706-1544 (United States); Center for Eukaryotic Structural Genomics (CESG), University of Wisconsin-Madison, WI 53706-1549 (United States)

    2005-08-01

    Adenosine 5′-monophosphate deaminase from A. thaliana has been crystallized in complex with coformycin 5′-phosphate. Diffraction data have been collected to 3.34 Å resolution. Adenosine 5′-monophosphate deaminase (AMPD) is a eukaryotic enzyme that converts adenosine 5′-monophosphate (AMP) to inosine 5′-monophosphate (IMP) and ammonia. AMPD from Arabidopsis thaliana (AtAMPD) was cloned into the baculoviral transfer vector p2Bac and co-transfected along with a modified baculoviral genome into Spodoptera frugiperda (Sf9) cells. The resulting recombinant baculovirus were plaque-purified, amplified and used to overexpress recombinant AtAMPD. Crystals of purified AtAMPD have been obtained to which coformycin 5′-phosphate, a transition-state inhibitor, is bound. Crystals belong to space group P6{sub 2}22, with unit-cell parameters a = b = 131.325, c = 208.254 Å, α = β = 90, γ = 120°. Diffraction data were collected to 3.34 Å resolution from a crystal in complex with coformycin 5′-phosphate and to 4.05 Å resolution from a crystal of a mercury derivative.

  1. Crystallization and preliminary X-ray diffraction analysis of the complex between a human anti-alpha toxin antibody fragment and alpha toxin.

    Science.gov (United States)

    Oganesyan, Vaheh; Barnes, Arnita; Tkaczyk, Christine; Ferguson, Andrew; Wu, Herren; Dall'Acqua, William F

    2013-03-01

    Staphylococcus aureus alpha toxin (AT) has been crystallized in complex with the Fab fragment of a human antibody (MEDI4893). This constitutes the first reported crystals of AT bound to an antibody. The monoclinic crystals belonged to space group P2₁, with unit-cell parameters a=85.52, b=148.50, c=93.82 Å, β=99.82°. The diffraction of the crystals extended to 2.56 Å resolution. The asymmetric unit contained two MEDI4893 Fab-AT complexes. This corresponds to a crystal volume per protein weight (VM) of 2.3 Å3 Da(-1) and a solvent content of 47%. The three-dimensional structure of this complex will contribute to an understanding of the molecular basis of the interaction of MEDI4893 with AT. It will also shed light on the mechanism of action of this antibody, the current evaluation of which in the field of S. aureus-mediated diseases makes it a particularly interesting case study. Finally, this study will provide the three-dimensional structure of AT in a monomeric state for the first time.

  2. Expression, purification, crystallization and preliminary X-ray analysis of the PaaI-like thioesterase SAV0944 from Staphylococcus aureus.

    Science.gov (United States)

    Khandokar, Yogesh B; Roman, Noelia; Smith, Kate M; Srivastava, Parul; Forwood, Jade K

    2014-02-01

    Staphylococcus aureus is the causative agent of many diseases, including meningitis, bacteraemia, pneumonia, food poisoning and toxic shock syndrome. Structural characterization of the PaaI-like thioesterase SAV0944 (SaPaaI) from S. aureus subsp. aureus Mu50 will aid in understanding its potential as a new therapeutic target by knowledge of its molecular details and cellular functions. Here, the recombinant expression, purification and crystallization of SaPaaI thioesterase from S. aureus are reported. This protein initially crystallized with the ligand coenzyme A using the hanging-drop vapour-diffusion technique with condition No. 40 of Crystal Screen from Hampton Research at 296 K. Optimal final conditions consisting of 24% PEG 4000, 100 mM sodium citrate pH 6.5, 12% 2-propanol gave single diffraction-quality crystals. These crystals diffracted to beyond 2 Å resolution at the Australian Synchrotron and belonged to space group P12(1)1, with unit-cell parameters a = 44.05, b = 89.05, c = 60.74 Å, β = 100.5°. Initial structure determination and refinement gave an R factor and R(free) of 17.3 and 22.0%, respectively, confirming a positive solution in obtaining phases using molecular replacement.

  3. Purification, crystallization and preliminary X-ray diffraction analysis of a soluble variant of the monoglyceride lipase Yju3p from the yeast Saccharomyces cerevisiae

    Energy Technology Data Exchange (ETDEWEB)

    Rengachari, Srinivasan; Aschauer, Philipp; Sturm, Christian; Oberer, Monika, E-mail: m.oberer@uni-graz.at [University of Graz, Humboldtstrasse 50/3, 8010 Graz (Austria)

    2015-01-28

    A soluble variant of the monoglyceride lipase Yju3p was successfully expressed, purified and crystallized. Diffraction data were collected to 2.4 Å resolution. The protein Yju3p is the orthologue of monoglyceride lipases in the yeast Saccharomyces cerevisiae. A soluble variant of this lipase termed s-Yju3p (38.3 kDa) was generated and purified to homogeneity by affinity and size-exclusion chromatography. s-Yju3p was crystallized in a vapour-diffusion setup at 293 K and a complete data set was collected to 2.4 Å resolution. The crystal form was orthorhombic (space group P2{sub 1}2{sub 1}2{sub 1}), with unit-cell parameters a = 77.2, b = 108.6, c = 167.7 Å. The asymmetric unit contained four molecules with a solvent content of 46.4%.

  4. Purification, crystallization and preliminary X-ray diffraction analysis of the putative ABC transporter ATP-binding protein from Thermotoga maritima

    Science.gov (United States)

    Ethayathulla, Abdul S.; Bessho, Yoshitaka; Shinkai, Akeo; Padmanabhan, Balasundaram; Singh, Tej P.; Kaur, Punit; Yokoyama, Shigeyuki

    2008-01-01

    Adenosine triphosphate (ATP) binding cassette transporters (ABC transporters) are ATP hydrolysis-dependent transmembrane transporters. Here, the overproduction, purification and crystallization of the putative ABC transporter ATP-binding protein TM0222 from Thermotoga maritima are reported. The protein was crystallized in the hexagonal space group P6422, with unit-cell parameters a = b = 148.49, c = 106.96 Å, γ = 120.0°. Assuming the presence of two molecules in the asymmetric unit, the calculated V M is 2.84 Å3 Da−1, which corresponds to a solvent content of 56.6%. A three-wavelength MAD data set was collected to 2.3 Å resolution from SeMet-substituted TM0222 crystals. Data sets were collected on the BL38B1 beamline at SPring-8, Japan. PMID:18540059

  5. Overproduction, purification, crystallization and preliminary X-ray analysis of the peroxiredoxin domain of a larger natural hybrid protein from Thermotoga maritima

    Energy Technology Data Exchange (ETDEWEB)

    Barbey, Carole, E-mail: carole.barbey@smbh.univ-paris13.fr [Laboratoire de Biophysique Moléculaire, Cellulaire et Tissulaire, UMR 7033, Université Paris 13, UFR SMBH, 74 Rue Marcel Cachin, 93017 Bobigny CEDEX (France); Rouhier, Nicolas [Unité Mixte de Recherches 1136 INRA UHP (Interaction Arbres Microorganismes), IFR 110, Nancy Université BP 239, 54506 Vandoeuvre-lès-Nancy CEDEX (France); Haouz, Ahmed [Plate-forme de Cristallogenèse et Diffraction des Rayons X, Institut Pasteur, 25 Rue du Dr Roux, 75724 Paris (France); Navaza, Alda [Laboratoire de Biophysique Moléculaire, Cellulaire et Tissulaire, UMR 7033, Université Paris 13, UFR SMBH, 74 Rue Marcel Cachin, 93017 Bobigny CEDEX (France); Jacquot, Jean-Pierre [Unité Mixte de Recherches 1136 INRA UHP (Interaction Arbres Microorganismes), IFR 110, Nancy Université BP 239, 54506 Vandoeuvre-lès-Nancy CEDEX (France); Laboratoire de Biophysique Moléculaire, Cellulaire et Tissulaire, UMR 7033, Université Paris 13, UFR SMBH, 74 Rue Marcel Cachin, 93017 Bobigny CEDEX (France)

    2008-01-01

    Crystals of the peroxiredoxin domain of a larger natural hybrid protein from T. maritima were obtained which diffracted to 2.9 Å resolution on a synchrotron source. Thermotoga maritima contains a natural hybrid protein constituted of two moieties: a peroxiredoxin domain at the N-terminus and a nitroreductase domain at the C-terminus. The peroxiredoxin (Prx) domain has been overproduced and purified from Escherichia coli cells. The recombinant Prx domain, which is homologous to bacterial Prx BCP and plant Prx Q, folds properly into a stable protein that possesses biological activity. The recombinant protein was crystallized and synchrotron data were collected to 2.9 Å resolution. The crystals belonged to the tetragonal space group I422, with unit-cell parameters a = b = 176.67, c = 141.20 Å.

  6. Plan for PLEX X-Ray Ablation Experiments and Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Latkowski, J F; Reyes, S

    2001-09-27

    PLEX is a Z-pinch based x-ray source that can produce x-rays with fluences (0.3-18 J/cm{sup 2}), pulselengths (10-30 ns), repetition rates (<10 Hz), and energies (50-500 eV) of interest for IFE chambers and optics. It provides an affordable, dedicated method to advance our understanding of x-ray damage to materials. The PLEX x-ray source will be used to experimentally validate and further develop the ABLATOR x-ray ablation code for use in inertial fusion energy (IFE) studies.

  7. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of macrophage growth locus A (MglA) protein from Francisella tularensis

    Energy Technology Data Exchange (ETDEWEB)

    Subburaman, P.; Austin, B.P.; Shaw, G.X.; Waugh, D.S.; Ji, X. (NCI)

    2010-11-03

    Francisella tularensis, a potential bioweapon, causes a rare infectious disease called tularemia in humans and animals. The macrophage growth locus A (MglA) protein from F. tularensis associates with RNA polymerase to positively regulate the expression of multiple virulence factors that are required for its survival and replication within macrophages. The MglA protein was overproduced in Escherichia coli, purified and crystallized. The crystals diffracted to 7.5 {angstrom} resolution at the Advanced Photon Source, Argonne National Laboratory and belonged to the hexagonal space group P6{sub 1} or P6{sub 5}, with unit-cell parameters a = b = 125, c = 54 {angstrom}.

  8. Expression, purification, crystallization and preliminary X-ray analysis of calmodulin in complex with the regulatory domain of the plasma-membrane Ca2+-ATPase ACA8

    DEFF Research Database (Denmark)

    Tidow, Henning; Hein, Kim Langmach; Bækgaard, Lone

    2010-01-01

    -bound calmodulin (Ca(2+)-CaM) to this tail and a conformational change that displaces the autoinhibitory tail from the catalytic domain. The complex between calmodulin and the regulatory domain of the plasma-membrane Ca(2+)-ATPase ACA8 from Arabidopsis thaliana has been crystallized. The crystals belonged to space......Plasma-membrane Ca(2+)-ATPases (PMCAs) are calcium pumps that expel Ca(2+) from eukaryotic cells to maintain overall Ca(2+) homoeostasis and to provide local control of intracellular Ca(2+) signalling. They are of major physiological importance, with different isoforms being essential, for example...

  9. Expression, purification, crystallization and preliminary X-ray analysis of calmodulin in complex with the regulatory domain of the plasma-membrane Ca2+-ATPase ACA8

    DEFF Research Database (Denmark)

    Tidow, Henning; Hein, Kim Langmach; Palmgren, Michael Broberg

    2010-01-01

    -bound calmodulin (Ca2+-CaM) to this tail and a conformational change that displaces the autoinhibitory tail from the catalytic domain. The complex between calmodulin and the regulatory domain of the plasma-membrane Ca2+-ATPase ACA8 from Arabidopsis thaliana has been crystallized. The crystals belonged to space......Plasma-membrane Ca2+-ATPases (PMCAs) are calcium pumps that expel Ca2+ from eukaryotic cells to maintain overall Ca2+ homoeostasis and to provide local control of intracellular Ca2+ signalling. They are of major physiological importance, with different isoforms being essential, for example...

  10. X-ray diffractometer configurations for thin film analysis

    Energy Technology Data Exchange (ETDEWEB)

    Haase, A. [Rich. Seifert and Co., Analytical X-ray Systems, Ahrensburg (Germany)

    1996-09-01

    A presentation of various configurations of focusing Seemann-Bohlin diffractometer, parafocusing Bragg-Brentano diffractometer and parallel beam are demonstrated. Equipped with different thin film attachments a comparison to conventional measurements are given. The application of different detector types like scintillation, gas proportional, electroluminescence (LUX) and solid state are described. Typical instrument set-ups for reflectometry, grazing incidence diffraction, total reflection, high resolution X-ray diffraction are explained. Different elements like slits, soller slits, pinhole collimators, crystal monochromators, monofiber (FOX) and polycapillaries (multifiber lens, Kumakhov lens`), flat or curved multilayer with constant or variable d-spacing, and their combinations are presented. The comparison of different beam conditioners in peak-to-background ratios are given. Wavelength dispersive scans show the energy discrimination possibilities of different beam optics.

  11. Integrated x-ray reflectivity measurements of elliptically curved pentaerythritol crystals

    Energy Technology Data Exchange (ETDEWEB)

    Haugh, M. J.; Jacoby, K. D.; Ross, P. W. [National Security Technologies, LLC, Livermore, California 94551 (United States); Regan, S. P.; Magoon, J.; Shoup, M. J. III [Laboratory for Laser Energetics, University of Rochester, Rochester, New York 14623 (United States); Barrios, M. A.; Emig, J. A.; Fournier, K. B. [Lawrence Livermore National Laboratory, Livermore, California 94550 (United States)

    2012-10-15

    The elliptically curved pentaerythritol (PET) crystals used in the Supersnout 2 x-ray spectrometer on the National Ignition Facility at Lawrence Livermore National Laboratory have been calibrated photometrically in the range of 5.5-16 keV. The elliptical geometry provides broad spectral coverage and minimizes the degradation of spectral resolution due to the finite source size. The reflectivity curve of the crystals was measured using a x-ray line source. The integrated reflectivity (R{sub I}) and width of its curve ({Delta}{Theta}) were the measurements of major interest. The former gives the spectrometer throughput, and the latter gives the spectrometer resolving power. Both parameters are found to vary considerably with the radius of curvature of the crystal and with spectral energy. The results are attributed to an enhanced mosaic effect due to the increase in curvature. There are also contributions from the crystal cleaving and gluing processes.

  12. Microbeam x-ray diffraction analysis of dental calculus.

    Science.gov (United States)

    Kani, T; Kani, M; Moriwaki, Y; Doi, Y

    1983-02-01

    The crystalline components of human dental calculus were investigated using microbeam x-ray diffraction analysis. Hydroxyapatite and octacalcium phosphate were most frequently found in that portion having porous and zonal structure. In the portion of the homogeneous illustration showing high calcification, whitlockite is a main component. Brushite was unexpectedly rare, and no calcite was detected in any portion of human dental calculus. The mechanism of the formation of dental calculus being considered in this paper is that octacalcium phosphate or brushite is formed during the initial stage of calcification of dental plaque, and is gradually hydrolyzed and transformed into hydroxyapatite and/or whitlockite.

  13. Elemental analysis by means of X-ray attenuation measurements

    Science.gov (United States)

    Cesareo, Roberto; Giannini, Marino

    1980-03-01

    Radioactive sources of 109Cd, 241Am and 57Co were employed to measure the attenuation coefficient of biological materials such as whole blood, red blood cells, plasma, urine, water and of materials of interest for computed tomography, such as plexiglas, polyethylene, nylon, teflon, etc. The experimental errors range between 0.3% and 1%. A method is also presented which allows quantitative analysis of materials by measuring their attenuation coefficient at various monoenergetic X-ray energies. As an example, attenuation measurements at 60 keV and 122 keV were employed in order to determine the concentration of lead and copper in silver alloys.

  14. Crystallization and preliminary X-ray analysis of a novel thermoalkalophilic poly(3-hydroxybutyrate) depolymerase (PhaZ7) from Paucimonas lemoignei

    Energy Technology Data Exchange (ETDEWEB)

    Kapetaniou, Evangelia G. [Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, Turku 20521 (Finland); Braaz, Reinhard; Jendrossek, Dieter [Institut fur Mikrobiologie, Universität Stuttgart (Germany); Papageorgiou, Anastassios C., E-mail: apapageo@btk.fi [Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, Turku 20521 (Finland)

    2005-05-01

    A novel thermoalkalophilic depolymerase, PhaZ7, from P. lemoignei was crystallized by the microdialysis technique. Crystals belong to space group C2 and diffract to 2.75 Å resolution at a synchrotron source. Polyhydroxyalkanoates (PHA) are biodegradable polyesters that have attracted commercial and academic interest as environmentally friendly materials. A number of enzymes are able to degrade polyhydroxyalkanoates to water-soluble products. PhaZ7 poly(3-hydroxybutyrate) (PHB) depolymerase (EC 3.1.1.75), a 342-amino-acid hydrolase from the PHA-degrading bacterium Paucimonas lemoignei, has been found to possess substrate specificity for amorphous PHA. PhaZ7 was crystallized by the microdialysis method. Thin rod-like crystals were grown in low ionic strength solution and found to belong to the monoclinic space group C2, with unit-cell parameters a = 225.8, b = 46.5, c = 171.3, β = 128.9°. A complete data set was collected to 2.75 Å resolution at 100 K using synchrotron radiation.

  15. PURIFICATION, CRYSTALLIZATION AND PRELIMINARY-X-RAY ANALYSIS OF PENICILLIN-BINDING PROTEIN-4 FROM ESCHERICHIA-COLI, A PROTEIN RELATED TO CLASS-A BETA-LACTAMASES

    NARCIS (Netherlands)

    THUNNISSEN, MMGM; FUSETTI, F; DEBOER, B; DIJKSTRA, BW

    1995-01-01

    Crystals of the penicillin binding protein 4 (PBP4) from Escherichia coli have been obtained at 37 degrees C from liquid to liquid diffusion experiments in capillaries. PBP4 was dissolved in a 1.0 M ammonium sulphate solution, buffered at pH 7.2, to a concentration of 5 mg/ml, and was layered on top

  16. Crystallization and preliminary X-ray analysis of human MTH1 complexed with two oxidized nucleotides, 8-oxo-dGMP and 2-oxo-dATP

    Energy Technology Data Exchange (ETDEWEB)

    Nakamura, Teruya; Kitaguchi, Yuki; Miyazawa, Masayuki [Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973 (Japan); Kamiya, Hiroyuki [Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812 (Japan); Toma, Sachiko; Ikemizu, Shinji [Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973 (Japan); Shirakawa, Masahiro [Graduate School of Engineering, Kyoto University, Kyoto 615-8510 (Japan); Nakabeppu, Yusaku [Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582 (Japan); Yamagata, Yuriko, E-mail: yamagata@gpo.kumamoto-u.ac.jp [Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973 (Japan)

    2006-12-01

    The complexes of human MTH1 with two oxidized nucleotides, 8-oxo-dGMP and 2-oxo-dATP, were crystallized. The crystals diffracted to 1.95 and 2.22 Å resolution, respectively. Human MutT homologue 1 (hMTH1) hydrolyzes a variety of oxidized purine nucleoside triphosphates, including 8-oxo-dGTP, 2-oxo-dATP, 2-oxo-ATP and 8-oxo-dATP, to their corresponding nucleoside monophosphates, while Esherichia coli MutT possesses prominent substrate specificity for 8-oxoguanine nucleotides. Three types of crystals were obtained corresponding to the following complexes: selenomethionine-labelled hMTH1 with 8-oxo-dGMP (SeMet hMTH1–8-oxo-dGMP), hMTH1 with 8-oxo-dGMP (hMTH1–8-oxo-dGMP) and hMTH1 with 2-oxo-dATP (hMTH1–2-oxo-dATP). Crystals of the SeMet hMTH1–8-oxo-dGMP complex belong to space group P4{sub 1}2{sub 1}2, with unit-cell parameters a = b = 45.8, c = 153.6 Å, and diffracted to 2.90 Å. Crystals of hMTH1–8-oxo-dGMP and hMTH1–2-oxo-dATP belong to space groups P2{sub 1} and P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 34.0, b = 59.0, c = 65.9 Å, β = 90.7° and a = 59.2, b = 67.3, c = 80.0 Å, respectively. Their diffraction data were collected at resolutions of 1.95 and 2.22 Å, respectively.

  17. Linear parabolic single-crystal diamond refractive lenses for synchrotron X-ray sources.

    Science.gov (United States)

    Terentyev, Sergey; Polikarpov, Maxim; Snigireva, Irina; Di Michiel, Marco; Zholudev, Sergey; Yunkin, Vyacheslav; Kuznetsov, Sergey; Blank, Vladimir; Snigirev, Anatoly

    2017-01-01

    Linear parabolic diamond refractive lenses are presented, designed to withstand high thermal and radiation loads coming from upgraded accelerator X-ray sources. Lenses were manufactured by picosecond laser treatment of a high-quality single-crystal synthetic diamond. Twelve lenses with radius of curvature at parabola apex R = 200 µm, geometrical aperture A = 900 µm and length L = 1.5 mm were stacked as a compound refractive lens and tested at the ESRF ID06 beamline. A focal spot of size 2.2 µm and a gain of 20 were measured at 8 keV. The lens profile and surface quality were estimated by grating interferometry and X-ray radiography. In addition, the influence of X-ray glitches on the focusing properties of the compound refractive lens were studied.

  18. Visualization of membrane protein crystals in lipid cubic phase using X-ray imaging.

    Science.gov (United States)

    Warren, Anna J; Armour, Wes; Axford, Danny; Basham, Mark; Connolley, Thomas; Hall, David R; Horrell, Sam; McAuley, Katherine E; Mykhaylyk, Vitaliy; Wagner, Armin; Evans, Gwyndaf

    2013-07-01

    The focus in macromolecular crystallography is moving towards even more challenging target proteins that often crystallize on much smaller scales and are frequently mounted in opaque or highly refractive materials. It is therefore essential that X-ray beamline technology develops in parallel to accommodate such difficult samples. In this paper, the use of X-ray microradiography and microtomography is reported as a tool for crystal visualization, location and characterization on the macromolecular crystallography beamlines at the Diamond Light Source. The technique is particularly useful for microcrystals and for crystals mounted in opaque materials such as lipid cubic phase. X-ray diffraction raster scanning can be used in combination with radiography to allow informed decision-making at the beamline prior to diffraction data collection. It is demonstrated that the X-ray dose required for a full tomography measurement is similar to that for a diffraction grid-scan, but for sample location and shape estimation alone just a few radiographic projections may be required.

  19. Crystallization and X-ray diffraction analysis of an l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii and a d-xylonate dehydratase from Caulobacter crescentus

    Energy Technology Data Exchange (ETDEWEB)

    Rahman, Mohammad Mubinur [University of Eastern Finland, Joensuu Campus, PO Box 111, FIN-80101 Joensuu (Finland); Andberg, Martina; Koivula, Anu [VTT Technical Research Centre of Finland Ltd, PO Box 1000, FIN-02044 VTT Espoo (Finland); Rouvinen, Juha; Hakulinen, Nina, E-mail: nina.hakulinen@uef.fi [University of Eastern Finland, Joensuu Campus, PO Box 111, FIN-80101 Joensuu (Finland)

    2016-07-13

    l-Arabinonate dehydratase and d-xylonate dehydratase from the IlvD/EDD family were crystallized by the vapour-diffusion method. Diffraction data sets were collected to resolutions of 2.40 and 2.66 Å from crystals of l-arabinonate dehydratase and d-xylonate dehydratase, respectively. l-Arabinonate dehydratase (EC 4.2.1.25) and d-xylonate dehydratase (EC 4.2.1.82) are two enzymes that are involved in a nonphosphorylative oxidation pathway of pentose sugars. l-Arabinonate dehydratase converts l-arabinonate into 2-dehydro-3-deoxy-l-arabinonate, and d-xylonate dehydratase catalyzes the dehydration of d-xylonate to 2-dehydro-3-deoxy-d-xylonate. l-Arabinonate and d-xylonate dehydratases belong to the IlvD/EDD family, together with 6-phosphogluconate dehydratases and dihydroxyacid dehydratases. No crystal structure of any l-arabinonate or d-xylonate dehydratase is available in the PDB. In this study, recombinant l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii (RlArDHT) and d-xylonate dehydratase from Caulobacter crescentus (CcXyDHT) were heterologously expressed in Escherichia coli and purified by the use of affinity chromatography followed by gel-filtration chromatography. The purified proteins were crystallized using the hanging-drop vapour-diffusion method at 293 K. Crystals of RlArDHT that diffracted to 2.40 Å resolution were obtained using sodium formate as a precipitating agent. They belonged to space group P2{sub 1}, with unit-cell parameters a = 106.07, b = 208.61, c = 147.09 Å, β = 90.43°. Eight RlArDHT molecules (two tetramers) in the asymmetric unit give a V{sub M} value of 3.2 Å{sup 3} Da{sup −1} and a solvent content of 62%. Crystals of CcXyDHT that diffracted to 2.66 Å resolution were obtained using sodium formate and polyethylene glycol 3350. They belonged to space group C2, with unit-cell parameters a = 270.42, b = 236.13, c = 65.17 Å, β = 97.38°. Four CcXyDHT molecules (a tetramer) in the asymmetric unit give a V{sub M

  20. Batch crystallization of rhodopsin for structural dynamics using an X-ray free-electron laser.

    Science.gov (United States)

    Wu, Wenting; Nogly, Przemyslaw; Rheinberger, Jan; Kick, Leonhard M; Gati, Cornelius; Nelson, Garrett; Deupi, Xavier; Standfuss, Jörg; Schertler, Gebhard; Panneels, Valérie

    2015-07-01

    Rhodopsin is a membrane protein from the G protein-coupled receptor family. Together with its ligand retinal, it forms the visual pigment responsible for night vision. In order to perform ultrafast dynamics studies, a time-resolved serial femtosecond crystallography method is required owing to the nonreversible activation of rhodopsin. In such an approach, microcrystals in suspension are delivered into the X-ray pulses of an X-ray free-electron laser (XFEL) after a precise photoactivation delay. Here, a millilitre batch production of high-density microcrystals was developed by four methodical conversion steps starting from known vapour-diffusion crystallization protocols: (i) screening the low-salt crystallization conditions preferred for serial crystallography by vapour diffusion, (ii) optimization of batch crystallization, (iii) testing the crystal size and quality using second-harmonic generation (SHG) imaging and X-ray powder diffraction and (iv) production of millilitres of rhodopsin crystal suspension in batches for serial crystallography tests; these crystals diffracted at an XFEL at the Linac Coherent Light Source using a liquid-jet setup.

  1. Crystallization and X-ray diffraction analysis of the β-ketoacyl-acyl carrier protein reductase FabG from Aquifex aeolicus VF5

    Energy Technology Data Exchange (ETDEWEB)

    Mao, Qilong [Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203 (United States); Duax, William L.; Umland, Timothy C., E-mail: umland@hwi.buffalo.edu [Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203 (United States); Department of Structural Biology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY (United States)

    2007-02-01

    FabG from A. aeolicus, a putative component of fatty-acid synthase II, has been overexpressed, purified and crystallized. Diffraction data have been collected to 1.8 Å resolution. The gene product of fabG from Aquifex aeolicus has been heterologously expressed in Escherichia coli. Purification of the protein took place using anion-exchange and size-exclusion chromatography and the protein was then crystallized. Diffraction data were collected to a maximum resolution of 1.8 Å and the initial phases were determined by molecular replacement. The A. aeolicus FabG protein is a putative β-ketoacyl-acyl carrier protein reductase. Structure–function studies of this protein are being performed as part of a larger project investigating naturally occurring deviations from highly conserved residues within the short-chain oxidoreductase (SCOR) family.

  2. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of a ferredoxin/flavodoxin-NADP(H) oxidoreductase (Bc0385) from Bacillus cereus.

    Science.gov (United States)

    Skråmo, Silje; Hersleth, Hans Petter; Hammerstad, Marta; Andersson, K Kristoffer; Røhr, Åsmund K

    2014-06-01

    Ferredoxin/flavodoxin-NADP(H) oxidoreductases (FNRs) are key enzymes involved in catalysing electron transfer between ferredoxins/flavodoxins and NAD(P)H/NAD(P)+. In Bacillus cereus there are three genes that may encode FNRs, and the Bc0385 FNR has been cloned, overexpressed, purified and successfully crystallized in its NADPH/NADP+-free form. Diffraction data have been collected to 2.5 Å resolution from crystals belonging to the orthorhombic space group P2₁2₁2, with unit-cell parameters a=57.2, b=164.3, c=95.0 Å, containing two FNR molecules in the asymmetric unit. The structure of the Bc0385 FNR has been solved by molecular replacement, and is a member of the homodimeric thioredoxin reductase-like class of FNRs.

  3. Crystallization and preliminary X-ray crystallographic analysis of MbtI, a protein essential for siderophore biosynthesis in Mycobacterium tuberculosis.

    Science.gov (United States)

    Harrison, Anthony J; Ramsay, Rochelle J; Baker, Edward N; Lott, J Shaun

    2005-01-01

    Mycobacterium tuberculosis, the causative agent of tuberculosis, depends on the secretion of salicylate-based siderophores called mycobactins for the acquisition of extracellular iron, which is essential for the growth and virulence of the bacterium. The protein MbtI is thought to be the isochorismate synthase enzyme responsible for the conversion of chorismate to isochorismate, the first step in the salicylate production required for mycobactin biosynthesis. MbtI has been overexpressed in Escherichia coli, purified and crystallized. The crystals diffract to a maximum resolution of 1.8 A. They belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 51.8, b = 163.4, c = 194.9 A, consistent with the presence of either two, three or four molecules in the asymmetric unit.

  4. Solving X-ray protein structures without a crystal: using X-ray Free Electron Laser, the fourth generation synchrotron light sources

    Institute of Scientific and Technical Information of China (English)

    Bo Huang

    2010-01-01

    @@ A synchrotron light source is a source of electromagnetic radiation artificially produced by specialized electron accelerators. Compared to the commonly used in-house X-ray sources, it is wavelength adjustable, much stronger and more focused. In the last two decades, synchrotron usage has become the mainstream for X-ray protein structure determination. Taking the advantage of micro-focus light beams of the third generation synchrotron, the size of a usable protein crystal for data collection decreases to micron level, which increases the rate of macromolecular structure determination to about 10 new protein data bank entries per day.

  5. Purification, crystallization and preliminary X-ray analysis of the outer membrane complex HasA–HasR from Serratia marcescens

    Energy Technology Data Exchange (ETDEWEB)

    Huché, Frédéric, E-mail: huche@pasteur.fr [Fachbereich Biologie, Universität Konstanz, 78457 Konstanz (Germany); Unité des Membranes Bactériennes, CNRS URA 2172, Département de Microbiologie Fondamentale et Médicale, Institut Pasteur, 25-28 Rue du Dr Roux, 75724 Paris CEDEX 15 (France); Delepelaire, Philippe; Wandersman, Cécile [Unité des Membranes Bactériennes, CNRS URA 2172, Département de Microbiologie Fondamentale et Médicale, Institut Pasteur, 25-28 Rue du Dr Roux, 75724 Paris CEDEX 15 (France); Welte, Wolfram [Fachbereich Biologie, Universität Konstanz, 78457 Konstanz (Germany)

    2006-01-01

    The expression, purification, and crystallization in space group P2{sub 1}2{sub 1}2{sub 1} of the complex HasA-HasR from S. marcescens are reported. Diffraction data have been collected and processed to 6.8 Å. Serratia marcescens is able to acquire iron using its haem-acquisition system (‘has’), which contains an outer membrane receptor HasR and a soluble haemophore HasA. After secretion, HasA binds free haem in the extracellular medium or extracts it from haemoproteins and delivers it to the receptor. Here, the crystallization of a HasA–HasR complex is reported. HasA and HasR have been overexpressed in Escherichia coli and the complex formed and crystallized. Small platelets and bunches of needles of dimensions 0.01 × 0.1 × 1 mm were obtained. A native data set has been collected to 6.8 Å.

  6. Crystallization and preliminary X-ray crystallographic analysis of MbtI, a protein essential for siderophore biosynthesis in Mycobacterium tuberculosis

    Energy Technology Data Exchange (ETDEWEB)

    Harrison, Anthony J. [School of Biological Sciences, University of Auckland, Private Bag 92-019, Auckland (New Zealand); Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92-019, Auckland (New Zealand); Ramsay, Rochelle J. [Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92-019, Auckland (New Zealand); Baker, Edward N.; Lott, J. Shaun, E-mail: s.lott@auckland.ac.nz [School of Biological Sciences, University of Auckland, Private Bag 92-019, Auckland (New Zealand); Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92-019, Auckland (New Zealand)

    2005-01-01

    MbtI, the putative isochorismate synthase essential for siderophore biosynthesis in M. tuberculosis, has been crystallized. Diffraction data have been collected to 1.8 Å resolution. Mycobacterium tuberculosis, the causative agent of tuberculosis, depends on the secretion of salicylate-based siderophores called mycobactins for the acquisition of extracellular iron, which is essential for the growth and virulence of the bacterium. The protein MbtI is thought to be the isochorismate synthase enzyme responsible for the conversion of chorismate to isochorismate, the first step in the salicylate production required for mycobactin biosynthesis. MbtI has been overexpressed in Escherichia coli, purified and crystallized. The crystals diffract to a maximum resolution of 1.8 Å. They belong to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 51.8, b = 163.4, c = 194.9 Å, consistent with the presence of either two, three or four molecules in the asymmetric unit.

  7. Indentation Size Effects in Single Crystal Copper as Revealed by Synchrotron X-ray Microdiffraction

    Energy Technology Data Exchange (ETDEWEB)

    Feng, G.; Budiman, A. S.; Nix, W. D.; Tamura, N.; Patel, J. R.

    2007-11-19

    The indentation size effect (ISE) has been observed in numerous nanoindentation studies on crystalline materials; it is found that the hardness increases dramatically with decreasing indentation size - a 'smaller is stronger' phenomenon. Some have attributed the ISE to the existence of strain gradients and the geometrically necessary dislocations (GNDs). Since the GND density is directly related to the local lattice curvature, the Scanning X-ray Microdiffraction ({mu}SXRD) technique, which can quantitatively measure relative lattice rotations through the streaking of Laue diffractions, can used to study the strain gradients. The synchrotron {mu}SXRD technique we use - which was developed at the Advanced Light Source (ALS), Berkeley Lab - allows for probing the local plastic behavior of crystals with sub-micrometer resolution. Using this technique, we studied the local plasticity for indentations of different depths in a Cu single crystal. Broadening of Laue diffractions (streaking) was observed, showing local crystal lattice rotation due to the indentation-induced plastic deformation. A quantitative analysis of the streaking allows us to estimate the average GND density in the indentation plastic zones. The size dependence of the hardness, as found by nanoindentation, will be described, and its correlation to the observed lattice rotations will be discussed.

  8. Crystallization and X-ray diffraction analysis of an l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii and a d-xylonate dehydratase from Caulobacter crescentus

    Science.gov (United States)

    Rahman, Mohammad Mubinur; Andberg, Martina; Koivula, Anu; Rouvinen, Juha; Hakulinen, Nina

    2016-01-01

    l-Arabinonate dehydratase (EC 4.2.1.25) and d-xylonate dehydratase (EC 4.2.1.82) are two enzymes that are involved in a nonphosphorylative oxidation pathway of pentose sugars. l-Arabinonate dehydratase converts l-arabinonate into 2-dehydro-3-deoxy-l-arabinonate, and d-xylonate dehydratase catalyzes the dehydration of d-xylonate to 2-dehydro-3-deoxy-d-xylonate. l-Arabinonate and d-xylonate dehydratases belong to the IlvD/EDD family, together with 6-phosphogluconate dehydratases and dihydroxyacid dehydratases. No crystal structure of any l-arabinonate or d-xylonate dehydratase is available in the PDB. In this study, recombinant l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii (RlArDHT) and d-xylonate dehydratase from Caulobacter crescentus (CcXyDHT) were heterologously expressed in Escherichia coli and purified by the use of affinity chromatography followed by gel-filtration chromatography. The purified proteins were crystallized using the hanging-drop vapour-diffusion method at 293 K. Crystals of RlArDHT that diffracted to 2.40 Å resolution were obtained using sodium formate as a precipitating agent. They belonged to space group P21, with unit-cell parameters a = 106.07, b = 208.61, c = 147.09 Å, β = 90.43°. Eight RlArDHT molecules (two tetramers) in the asymmetric unit give a V M value of 3.2 Å3 Da−1 and a solvent content of 62%. Crystals of CcXyDHT that diffracted to 2.66 Å resolution were obtained using sodium formate and polyethylene glycol 3350. They belonged to space group C2, with unit-cell parameters a = 270.42, b = 236.13, c = 65.17 Å, β = 97.38°. Four CcXyDHT molecules (a tetramer) in the asymmetric unit give a V M value of 4.0 Å3 Da−1 and a solvent content of 69%. PMID:27487924

  9. Crystallization and X-ray diffraction analysis of an L-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii and a D-xylonate dehydratase from Caulobacter crescentus.

    Science.gov (United States)

    Rahman, Mohammad Mubinur; Andberg, Martina; Koivula, Anu; Rouvinen, Juha; Hakulinen, Nina

    2016-08-01

    L-Arabinonate dehydratase (EC 4.2.1.25) and D-xylonate dehydratase (EC 4.2.1.82) are two enzymes that are involved in a nonphosphorylative oxidation pathway of pentose sugars. L-Arabinonate dehydratase converts L-arabinonate into 2-dehydro-3-deoxy-L-arabinonate, and D-xylonate dehydratase catalyzes the dehydration of D-xylonate to 2-dehydro-3-deoxy-D-xylonate. L-Arabinonate and D-xylonate dehydratases belong to the IlvD/EDD family, together with 6-phosphogluconate dehydratases and dihydroxyacid dehydratases. No crystal structure of any L-arabinonate or D-xylonate dehydratase is available in the PDB. In this study, recombinant L-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii (RlArDHT) and D-xylonate dehydratase from Caulobacter crescentus (CcXyDHT) were heterologously expressed in Escherichia coli and purified by the use of affinity chromatography followed by gel-filtration chromatography. The purified proteins were crystallized using the hanging-drop vapour-diffusion method at 293 K. Crystals of RlArDHT that diffracted to 2.40 Å resolution were obtained using sodium formate as a precipitating agent. They belonged to space group P21, with unit-cell parameters a = 106.07, b = 208.61, c = 147.09 Å, β = 90.43°. Eight RlArDHT molecules (two tetramers) in the asymmetric unit give a VM value of 3.2 Å(3) Da(-1) and a solvent content of 62%. Crystals of CcXyDHT that diffracted to 2.66 Å resolution were obtained using sodium formate and polyethylene glycol 3350. They belonged to space group C2, with unit-cell parameters a = 270.42, b = 236.13, c = 65.17 Å, β = 97.38°. Four CcXyDHT molecules (a tetramer) in the asymmetric unit give a VM value of 4.0 Å(3) Da(-1) and a solvent content of 69%.

  10. Crystallization and X-ray diffraction analysis of the beta-ketoacyl-acyl carrier protein reductase FabG from Aquifex aeolicus VF5.

    Science.gov (United States)

    Mao, Qilong; Duax, William L; Umland, Timothy C

    2007-02-01

    The gene product of fabG from Aquifex aeolicus has been heterologously expressed in Escherichia coli. Purification of the protein took place using anion-exchange and size-exclusion chromatography and the protein was then crystallized. Diffraction data were collected to a maximum resolution of 1.8 A and the initial phases were determined by molecular replacement. The A. aeolicus FabG protein is a putative beta-ketoacyl-acyl carrier protein reductase. Structure-function studies of this protein are being performed as part of a larger project investigating naturally occurring deviations from highly conserved residues within the short-chain oxidoreductase (SCOR) family.

  11. Expression, crystallization and preliminary X-ray crystallographic analysis of D-alanine-D-alanine ligase from OXA-23-producing Acinetobacter baumannii K0420859.

    Science.gov (United States)

    Huynh, Kim-Hung; Tran, Huyen-Thi; Pham, Tan-Viet; Ngo, Ho-Phuong-Thuy; Cha, Sun-Shin; Chung, Kyung Min; Lee, Sang Hee; Kang, Lin-Woo

    2014-04-01

    Acinetobacter baumannii causes bacteraemia, pneumonia, other respiratory-tract and urinary-tract infections in humans. OXA-23 carbapenemase-producing A. baumannii K0420859 (A. baumannii OXA-23) is resistant to carbapenem, a common antibacterial drug. To develop an efficient and novel antibacterial drug against A. baumannii OXA-23, D-alanine-D-alanine ligase, which is essential in bacterial cell-wall synthesis, is of interest. Here, the D-alanine-D-alanine ligase (AbDdl) gene from A. baumannii OXA-23 was cloned and expressed, and the AbDdl protein was purified and crystallized; this enzyme can be used as a novel target for an antibacterial drug against A. baumannii OXA-23. The AbDdl crystal diffracted to a resolution of 2.8 Å and belonged to the orthorhombic space group P212121, with unit-cell parameters a = 113.4, b = 116.7, c = 176.5 Å, a corresponding VM of 2.8 Å(3) Da(-1) and a solvent content of 56.3%, and six protomers in the asymmetric unit.

  12. Crystallization and preliminary X-ray crystallographic analysis of the small subunit of the heterodimeric laccase POXA3b from Pleurotus ostreatus.

    Science.gov (United States)

    Ferraroni, Marta; Scozzafava, Andrea; Ullah, Sana; Tron, Thierry; Piscitelli, Alessandra; Sannia, Giovanni

    2014-01-01

    Laccases are multicopper oxidases of great biotechnological potential. While laccases are generally monomeric glycoproteins, the white-rot fungus Pleurotus ostreatus produces two closely related heterodimeric isoenzymes composed of a large subunit, homologous to the other fungal laccases, and a small subunit. The sequence of the small subunit does not show significant homology to any other protein or domain of known function and consequently its function is unknown. The highest similarity to proteins of known structure is to a putative enoyl-CoA hydratase/isomerase from Acinetobacter baumannii, which shows an identity of 27.8%. Diffraction-quality crystals of the small subunit of the heterodimeric laccase POXA3b (sPOXA3b) from P. ostreatus were obtained using the sitting-drop vapour-diffusion method at 294 K from a solution consisting of 1.8 M sodium formate, 0.1 M Tris-HCl pH 8.5. The crystals belonged to the tetragonal space group P4(1)2(1)2 or P4(3)2(1)2, with unit-cell parameters a = 126.6, c = 53.9 Å. The asymmetric unit contains two molecules related by a noncrystallographic twofold axis. A complete data set extending to a maximum resolution of 2.5 Å was collected at 100 K using a wavelength of 1.140 Å.

  13. Preparation, Crystallization and X-ray Diffraction Analysis to 1.5 A Resolution of Rat Cysteine Dioxygenase, a Mononuclear Iron Enzyme Responsible for Cysteine Thiol Oxidation

    Energy Technology Data Exchange (ETDEWEB)

    Simmons,C.; Hao, Q.; Stipanuk, M.

    2005-01-01

    Cysteine dioxygenase (CDO; EC 1.13.11.20) is an {approx}23 kDa non-heme iron metalloenzyme that is responsible for the oxidation of cysteine by O2, yielding cysteinesulfinate. CDO catalyzes the first step in the conversion of cysteine to taurine, as well as the first step in the catabolism of cysteine to pyruvate plus sulfate. Recombinant rat CDO was heterologously expressed, purified and crystallized. The protein was expressed as a fusion protein bearing a polyhistidine tag to facilitate purification, a thioredoxin tag to improve solubility and a factor Xa cleavage site to permit removal of the entire N-terminus, leaving only the 200 amino acids inherent to the native protein. A multi-step purification scheme was used to achieve >95% purity of CDO. The optimal CDO crystals diffracted to 1.5 Angstroms resolution and belonged to space group P4{sub 3}2{sub 1}2 or P4{sub 1}2{sub 1}2, with unit-cell parameters a = b = 57.55, c = 123.06 Angstrom, {alpha} = {beta} = {gamma} = 90. CDO shows little homology to any other proteins; therefore, the structure of the enzyme will be determined by ab initio phasing using a selenomethionyl derivative.

  14. Overproduction, crystallization and X-ray diffraction data analysis of ectoine synthase from the cold-adapted marine bacterium Sphingopyxis alaskensis.

    Science.gov (United States)

    Kobus, Stefanie; Widderich, Nils; Hoeppner, Astrid; Bremer, Erhard; Smits, Sander H J

    2015-08-01

    Ectoine biosynthetic genes (ectABC) are widely distributed in bacteria. Microorganisms that carry them make copious amounts of ectoine as a cell protectant in response to high-osmolarity challenges. Ectoine synthase (EctC; EC 4.2.1.108) is the key enzyme for the production of this compatible solute and mediates the last step of ectoine biosynthesis. It catalyzes the ring closure of the cyclic ectoine molecule. A codon-optimized version of ectC from Sphingopyxis alaskensis (Sa) was used for overproduction of SaEctC protein carrying a Strep-tag II peptide at its carboxy-terminus. The recombinant SaEctC-Strep-tag II protein was purified to near-homogeneity from Escherichia coli cell extracts by affinity chromatography. Size-exclusion chromatography revealed that it is a dimer in solution. The SaEctC-Strep-tag II protein was crystallized using the sitting-drop vapour-diffusion method and crystals that diffracted to 1.0 Å resolution were obtained.

  15. High resolution X-ray diffraction studies on unirradiated and irradiated strontium hexaferrite crystals

    Indian Academy of Sciences (India)

    Balwinder Kaur; Monita Bhat; F Licci; Ravi Kumar; K K Bamzai; P N Kotru

    2012-04-01

    High-resolution X-ray diffraction technique, employing a three-crystal monochromator–collimator combination is used to study the irradiation induced defects in flux grown Sr-hexaferrite crystals irradiated with 50 MeV Li3+ ion beams at room temperature with a fluence value of 1 × 1014 ions/cm2. The diffraction curves of the irradiated crystals suggest the possibility of creation of low angle grain boundaries and other point/clusters of defects causing amorphization in the irradiated crystals. The perfection of the irradiated and unirradiated (0001) cleaved surfaces of the crystals is studied using the bulk method of X-ray topography. The topographs supplement the findings suggestive of modifications in the crystalline quality of SrFe12O19 on irradiation with SHI of Li3+. Etching of the (0001) cleaved surfaces in H3PO4 at 120°C suggests that the dissolution characteristics of the surfaces get affected on irradiation with SHI of Li3+, besides supporting the findings of HRXRD and X-ray topography regarding modifications in the perfection of SrFe12O19 on irradiation.

  16. Development of elemental analysis by muonic X-ray measurement in J-PARC

    Science.gov (United States)

    Ninomiya, K.; Nagatomo, T.; Kubo, K. M.; Strasser, P.; Kawamura, N.; Shimomura, K.; Miyake, Y.; Saito, T.; Higemoto, W.

    2010-04-01

    Muon irradiation and muonic X-ray detection can be applied to non-destructive elemental analysis. In this study, in order to develop the elemental analysis by muonic X-ray measurement we constructed a new X-ray measuring system in J-PARC muon facility. We performed muon irradiation for Tempo-koban (Japanese old coin) for test experiment of elemental analysis. Muonic X-rays originating from muon transition in muonic silver and gold atoms were identified. The contents of Tempo-koban (Au:56%) was determined by muonic X-ray intensities.

  17. Synthesis, X-ray crystal structures, thermal and electrochemical properties of thiosemicarbazidatodioxouranium(VI) complexes.

    Science.gov (United States)

    Sahin, Musa; Koca, Atıf; Ozdemir, Namık; Dinçer, Muharrem; Büyükgüngör, Orhan; Bal-Demirci, Tülay; Ulküseven, Bahri

    2010-11-14

    The stable uranyl complexes, [UO(2)(L)C(9)H(19)OH], were obtained from 3,5-dichlorosalicyl-(L(I)) and salicyl-aldehyde-S-propyl-thiosemicarbazones (L(II)) with substituted-salicylaldehyde in nonyl alcohol. The structures of the complexes have been characterized by elemental analysis, IR, (1)H NMR, conductivity, magnetic moment measurements, cyclic voltammetry, thermal gravimetric analysis and single crystal X-ray diffraction technique. The U(VI) centre is seven-coordinated in a distorted pentagonal bipyramidal geometry. The relative orientations of the nonyl alcohol and S-propyl group in the title complexes are completely different due to different crystal packing. Electrochemical behaviors of the thiosemicarbazone ligands and the uranyl complexes were studied using cyclic voltammetry and square wave voltammetry. Redox processes of the compounds are significantly influenced by the central metal ions and the nature of substituents on the thiosemicarbazones, which are important factors in controlling the redox properties. In situ spectroelectrochemical studies were employed to determine the colors and spectra of electro-generated species of the complexes.

  18. Single-crystal X-ray diffraction study of synthetic sodium-hydronium jarosite

    Science.gov (United States)

    Najorka, Jens; Lewis, James M. T.; Spratt, John; Sephton, Mark A.

    2016-05-01

    Na-H3O jarosite was synthesized hydrothermally at 413 K for 8 days and investigated using single-crystal X-ray diffraction (XRD) and electron microprobe analysis (EMPA). The chemical composition of the studied crystal is [Na0.57(3) (H3O)0.36 (H2O)0.07]A Fe2.93(3) (SO4)2 (OH)5.70 (H2O)0.30, and Fe deficiency was confirmed by both EMPA and XRD analysis. The single-crystal XRD data were collected at 298 and 102 K, and crystal structures were refined in space group Roverline{3}m. The room-temperature data match structural trends of the jarosite group, which vary linearly with the c axis. The low-temperature structure at 102 K shows an anisotropic decrease in the unit cell parameters, with c and a decreasing by 0.45 and 0.03 %, respectively. Structural changes are mainly confined to the A site environment. Only minor changes occur in FeO6 and SO4 polyhedra. The structure responds upon cooling by increasing bond length distortion and by decreasing quadratic elongation of the large AO12 polyhedra. The structural parameters at low temperature follow very similar patterns to structural changes that correspond to compositional variation in the jarosite group, which is characterised by the flexibility of AO12 polyhedra and rigidity of Fe(OH)4O2-SO4 layers. The most flexible areas in the jarosite structure are localized at AO12 edges that are not shared with neighbouring FeO6 octahedra. Importantly, for the application of XRD in planetary settings, the temperature-related changes in jarosite can mimic compositional change.

  19. A multi-cone x-ray imaging Bragg crystal spectrometer

    Science.gov (United States)

    Bitter, Manfred; Hill, K. W.; Gao, Lan; Efthimion, P. C.; Delgado-Aparicio, L.; Lazerson, S.; Pablant, N.

    2016-10-01

    In a recent article, see, we described a new x-ray imaging Bragg crystal spectrometer, which - in combination with a streak camera or a gated strip detector - can be used for time-resolved measurements of x-ray line spectra at the National Ignition Facility (NIF) and other high power laser facilities. The main advantage of this instrument is that it produces perfect images of a point source for each wavelength in a selectable spectral range and that the detector plane can be inclined by an arbitrary angle with respect to the crystal surface. These unique imaging properties are obtained by bending the x-ray diffracting crystal into a certain shape, which is generated by arranging multiple cones with different aperture angles on a common nodal line. In this paper, we present results from optical tests of these multi-cone structures and numerical results on the deteriorations of the spectral and spatial resolutions that may be caused by potential misalignments of the source, crystal, and detector. Princeton Plasma Physics Laboratory.

  20. Crystallization and preliminary X-ray diffraction experiments of arylmalonate decarboxylase from Alcaligenes bronchisepticus

    Energy Technology Data Exchange (ETDEWEB)

    Nakasako, Masayoshi, E-mail: nakasako@phys.keio.ac.jp [Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Kanagawa 223-8522 (Japan); The RIKEN Harima Institute/SPring-8, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148 (Japan); Obata, Rika; Okubo, Ryosuke; Nakayama, Shyuichi [Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Kanagawa 223-8522 (Japan); Miyamoto, Kenji; Ohta, Hiromichi [Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Kanagawa 223-8522 (Japan); Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Kanagawa 223-8522 (Japan)

    2008-07-01

    Crystals of arylmalonate decarboxylase from A. bronchisepticus were obtained which diffracted X-rays to a resolution of at least 3.0 Å. Arylmalonate decarboxylase catalyses the enantioselective decarboxylation of α-aryl-α-methylmalonates to produce optically pure α-arylpropionates. The enzyme was crystallized with ammonium sulfate under alkaline pH conditions with the aim of understanding the mechanism of the enantioselective reaction. X-ray diffraction data collected to a resolution of 3.0 Å at cryogenic temperature showed that the crystals belonged to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 83.13, b = 99.62, c = 139.64 Å. This suggested that the asymmetric unit would contain between four and six molecules. Small-angle X-ray scattering revealed that the enzyme exists as a monomer in solution. Thus, the assembly of molecules in the asymmetric unit was likely to have been induced during the crystallization process.

  1. Pyrazolato metal complexes: synthesis, characterization and X-ray crystal structures of rhenium(I) derivaties

    Energy Technology Data Exchange (ETDEWEB)

    Ardizzoia, G.A; LaMonica, G.; Maspero, A. [Milan Univ. (Italy). Dipt. di Chimica Inorganica, Metallorganica e Analitica; Moret, M.; Masciocchi, N. [Milan Univ. (Italy). Dipt. di Chimica Strutturale e Stereochimica Inorganica

    1998-10-01

    The mononuclear complexes [Re(CO){sub 3}(Hpz){sub 2}Br] (1) and [Re(CO){sub 3}(Hdmpz){sub 2}Br] (2) were obtained by treating [Re(CO){sub 5}Br] with pyrazole (Hpz) or 3,5-dimethylpyrazole (Hdmpz). Complex 1 reacted with triethylamine affording a mixture of the ionic dinuclear derivative (Et{sub 3}NH)[Re{sub 2}(CO){sub 6}(pz){sub 2}Br] (3) and of the mononuclear species [Re(CO){sub 3}(Hpz){sub 2}(pz)] (4). Complex 4 was obtained in a pure form by carrying out the reaction in the presence of excess free pyrazole. Treatment of 4 with pyridine afforded the [Re(CO){sub 3}(py)(Hpz)(pz)] species (6). The analogues of 4 and 6 with Hdmpz, i.e. [Re(CO){sub 3}(Hdmpz){sub 2}(dmpz)] (7) and [Re(CO){sub 3}(py)(Hdmpz)(dmpz)] (8) were also synthesized. All species were characterized in solution by {sup 1}H-NMR spectroscopy, while the crystal structures of complexes 1, 3, 4 and 6 were determined by single-crystal X-ray diffraction analysis. The [(CO){sub 3}Re({mu}-pz){sub 2}({mu}-Br)Re(CO){sub 3}]{sup -} anion represents the first structurally characterized species containing rhenium(I) atoms bridged by mu-pyrazolate ligands. (orig.)

  2. Preparation, Spectroscopy, Physicochemical Properties and X-ray Structure Analysis of 3,4,5-Trimethoxy N(2-hydroxybenzylidene aniline

    Directory of Open Access Journals (Sweden)

    Kodjo Charles Guillaume

    2009-01-01

    Full Text Available 3,4,5-Trimethoxy N-(salicylidene aniline was synthesized and characterized by IR spectroscopy, 1H NMR and x-ray single crystal analysis. UV-visible spectroscopy was used for physicochemical tests. X-ray data reveals that the crystalline network cohesion of this compound is essentially assured by CH/pi type hydrogen bounds. It crystallized in the orthorhombic Pbcn space group. Electronic spectroscopy shows that the title compound doesn't present photochromic property but thermochromic one. Intermolecular interactions analysis confirms for this compound a thermochromic structural predisposition.

  3. Barbiturate bearing aroylhydrazine derivatives: Synthesis, NMR investigations, single crystal X-ray studies and biological activity

    Science.gov (United States)

    Giziroglu, Emrah; Sarikurkcu, Cengiz; Aygün, Muhittin; Basbulbul, Gamze; Soyleyici, H. Can; Firinci, Erkan; Kirkan, Bulent; Alkis, Ayse; Saylica, Tayfur; Biyik, Halil

    2016-03-01

    A series of barbituric acid aroylhydrazine derivatives have been prepared from their corresponding 1,3-dimethyl-5-acetyl barbituric acid and aroylhydrazines. All compounds have been fully characterized by using FT-IR, multinuclear NMR (1H, 13C) and Mass (MS) spectrometry. We also describe the X-ray crystal structure of 3a, which crystallizes in the monoclinic P21/n space group. The crystal structure is stabilized with infinite linear chains of dimeric units. Furthermore, all compounds were investigated for their tyrosinase inhibition, antioxidative and antimicrobial activies. The results from biological activity assays have shown that all of compounds have excellent antioxidant, significant tyrosinase inhibition and moderate antimicrobial activity.

  4. Crystallization and preliminary X-ray diffraction data of alpha-galactosidase from Saccharomyces cerevisiae.

    Science.gov (United States)

    Fernández-Leiro, Rafael; Pereira-Rodríguez, Angel; Cerdán, M Esperanza; Becerra, Manuel; Sanz-Aparicio, Juliana

    2010-01-01

    Saccharomyces cerevisiae alpha-galactosidase is a highly glycosylated extracellular protein that catalyzes the hydrolysis of alpha-galactosidic linkages in various glucids. Its enzymatic activity is of interest in many food-related industries and has biotechnological applications. Glycosylated and in vitro deglycosylated protein samples were both assayed for crystallization, but only the latter gave good-quality crystals that were suitable for X-ray crystallography. The crystals belonged to space group P42(1)2, with unit-cell parameters a = b = 101.24, c = 111.52 A. A complete diffraction data set was collected to 1.95 A resolution using a synchrotron source.

  5. Crystallization and X-ray diffraction of spray-dried and freeze-dried amorphous lactose.

    Science.gov (United States)

    Haque, Md Kamrul; Roos, Yrjö H

    2005-02-07

    Crystallization of spray-dried and freeze-dried amorphous lactose over different relative vapor pressures (RVP) and storage times was studied. Crystallization was observed from increasing peak intensities in X-ray diffraction patterns. Lactose was crystallized in the samples stored at RVP of 44.1% and above in both types of dehydrated powders. The rate of crystallization increased with increasing RVP and storage time. Similar crystallization behavior of both spray-dried and freeze-dried lactose was observed. Lactose crystallized as alpha-lactose monohydrate, anhydrous beta-lactose, and the anhydrous form of alpha- and beta-lactose in a molar ratio of 5:3 and 4:1 in both spray-dried and freeze-dried forms. Peak intensities of X-ray diffraction patterns for anhydrous beta-lactose were decreased, and for alpha-lactose monohydrate increased with increasing storage RVP and time. The crystallization data were successfully modeled using Avrami equation at RVP of 54.5% and above. The crystallization data obtained is helpful in understanding and predicting storage stability of lactose-containing food and pharmaceutical products.

  6. Large-surface-area diamond (111) crystal plates for applications in high-heat-load wavefront-preserving x-ray crystal optics

    CERN Document Server

    Stoupin, S; Butler, J E; Kolyadin, A V; Katrusha, A

    2016-01-01

    We report fabrication and results of high-resolution X-ray topography characterization of diamond single crystal plates with a large surface area (10$\\times$10 mm$^2$) and (111) crystal surface orientation for applications in high-heat-load X-ray crystal optics. The plates were fabricated by laser cutting of the (111) facets of diamond crystals grown using high-pressure high-temperature method. The intrinsic crystal quality of a selected 3$\\times$7~mm$^2$ crystal region of one of the studied samples was found to be suitable for applications in wavefront-preserving high-heat-load crystal optics. The wavefront characterization was performed using sequential X-ray diffraction topography in the pseudo plane wave configuration and data analysis using rocking curve topography. The variation of the rocking curve width and peak position measured with a spatial resolution of 13$\\times$13 $\\mu m^2$ over the selected region were found to be less than one microradian.

  7. Large-surface-area diamond (111) crystal plates for applications in high-heat-load wavefront-preserving X-ray crystal optics.

    Science.gov (United States)

    Stoupin, Stanislav; Antipov, Sergey; Butler, James E; Kolyadin, Alexander V; Katrusha, Andrey

    2016-09-01

    Fabrication and results of high-resolution X-ray topography characterization of diamond single-crystal plates with large surface area (10 mm × 10 mm) and (111) crystal surface orientation for applications in high-heat-load X-ray crystal optics are reported. The plates were fabricated by laser-cutting of the (111) facets of diamond crystals grown using high-pressure high-temperature methods. The intrinsic crystal quality of a selected 3 mm × 7 mm crystal region of one of the studied samples was found to be suitable for applications in wavefront-preserving high-heat-load crystal optics. Wavefront characterization was performed using sequential X-ray diffraction topography in the pseudo plane wave configuration and data analysis using rocking-curve topography. The variations of the rocking-curve width and peak position measured with a spatial resolution of 13 µm × 13 µm over the selected region were found to be less than 1 µrad.

  8. Time series analysis of bright galactic X-ray sources

    DEFF Research Database (Denmark)

    Priedhorsky, W. C.; Brandt, Søren; Lund, Niels

    1995-01-01

    We analyze 70 to 110 day data sets from eight bright galactic X-ray binaries observed by WATCH/Eureca, in search of periodic variations. We obtain new epochs for the orbital variation of Cyg X-3 and 4U 1700-37, and confirmation of a dip in Cyg X-1 at superior conjunction of the X-ray star. No evi...

  9. Feasibility study of total reflection X-ray fluorescence analysis using a liquid metal jet X-ray tube

    Energy Technology Data Exchange (ETDEWEB)

    Maderitsch, A.; Smolek, S. [Atominstitut, Vienna University of Technology, Stadionallee 2, 1020 Wien (Austria); Wobrauschek, P., E-mail: wobi@ati.ac.at [Atominstitut, Vienna University of Technology, Stadionallee 2, 1020 Wien (Austria); Streli, C. [Atominstitut, Vienna University of Technology, Stadionallee 2, 1020 Wien (Austria); Takman, P. [Excillum AB, Finlandsgatan 14, 164 74 Kista (Sweden)

    2014-09-01

    Total reflection X-ray spectroscopy (TXRF) is a powerful analytical technique for qualitative and quantitative analysis of trace and ultratrace elements in a sample with lower limits of detection (LLDs) of pg/g to ng/g in concentration and absolute high fg levels are attainable. Several X-ray sources, from low power (few W), 18 kW rotating anodes to synchrotron radiation, are in use for the excitation and lead accordingly to their photon flux delivered on the sample the detection limits specified. Not only the power, but also the brilliance and focal shape are of importance for TXRF. A microfocus of 50–100 μm spot size or the line focus of diffraction tubes is best suited. Excillum developed a new approach in the design of a source: the liquid metal jet anode. In this paper the results achieved with this source are described. A versatile TXRF spectrometer with vacuum chamber designed at Atominstitut was used for the experiments. A multilayer monochromator selecting the intensive Ga-Kα radiation was taken and the beam was collimated by 50 μm slits. Excellent results regarding geometric beam stability, high fluorescence intensities and low background were achieved leading to detection limits in the high fg range for Ni. A 100 mm{sup 2} silicon drift detector (SDD) collimated to 80 mm{sup 2} was used to collect the fluorescence radiation. The results from measurements on single element samples are presented. - Highlights: • Using a new X-ray source for TXRF • Liquid metal jet X-ray source from Excillum • Offers improvements for lab based TXRF spectrometers • Can also be important for related techniques.

  10. Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser

    OpenAIRE

    2015-01-01

    G protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signaling to numerous G protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveal...

  11. Heteroaryl Chalcones: Design, Synthesis, X-ray Crystal Structures and Biological Evaluation

    OpenAIRE

    2013-01-01

    Chalcone derivatives have attracted increasing attention due to their numerous pharmacological activities. Changes in their structures have displayed high degree of diversity that has proven to result in a broad spectrum of biological activities. The present study highlights the synthesis of some halogen substituted chalcones 3(a–i) containing the 5-chlorothiophene moiety, their X-ray crystal structures and the evaluation of possible biological activities such as antibacterial, antifungal and...

  12. Guiding synchrotron X-ray diffraction by multimodal video-rate protein crystal imaging

    OpenAIRE

    Newman, Justin A.; ZHANG, Shijie; Sullivan, Shane Z.; Dow, Ximeng Y.; Becker, Michael; Sheedlo, Michael J.; Stepanov, Sergey; Carlsen, Mark S.; Everly, R. Michael; Das, Chittaranjan; Fischetti, Robert F.; Simpson, Garth J.

    2016-01-01

    Synchronous digitization, in which an optical sensor is probed synchronously with the firing of an ultrafast laser, was integrated into an optical imaging station for macromolecular crystal positioning prior to synchrotron X-ray diffraction. Using the synchronous digitization instrument, second-harmonic generation, two-photon-excited fluorescence, one-photon-excited fluorescence, two-photon-excited ultraviolet fluorescence and bright field by laser transmittance were all acquired with perfect...

  13. Calculations and surface quality measurements of high-asymmetry angle x-ray crystal monochromators for advanced x-ray imaging and metrological applications

    Science.gov (United States)

    Zápražný, Zdenko; Korytár, Dušan; Jergel, Matej; Šiffalovič, Peter; Dobročka, Edmund; Vagovič, Patrik; Ferrari, Claudio; Mikulík, Petr; Demydenko, Maksym; Mikloška, Marek

    2015-03-01

    We present the numerical optimization and the technological development progress of x-ray optics based on asymmetric germanium crystals. We show the results of several basic calculations of diffraction properties of germanium x-ray crystal monochromators and of an analyzer-based imaging method for various asymmetry factors using an x-ray energy range from 8 to 20 keV. The important parameter of highly asymmetric monochromators as image magnifiers or compressors is the crystal surface quality. We have applied several crystal surface finishing methods, including advanced nanomachining using single-point diamond turning (SPDT), conventional mechanical lapping, chemical polishing, and chemomechanical polishing, and we have evaluated these methods by means of atomic force microscopy, diffractometry, reciprocal space mapping, and others. Our goal is to exclude the chemical etching methods as the final processing technique because it causes surface undulations. The aim is to implement very precise deterministic methods with a control of surface roughness down to 0.1 nm. The smallest roughness (˜0.3 nm), best planarity, and absence of the subsurface damage were observed for the sample which was machined using an SPDT with a feed rate of 1 mm/min and was consequently polished using a fine polishing 15-min process with a solution containing SiO2 nanoparticles (20 nm).

  14. High resolution X-ray spherically bent crystal spectrometer for laser-produced plasma diagnostics

    Institute of Scientific and Technical Information of China (English)

    Shali Xiao; Hongjian Wang; Jun Shi; Changhuan Tang; Shenye Liu

    2009-01-01

    A new high spectral resolution crystal spectrometer is designed to measure very low emissive X-ray spectra of laser-produced plasma in 0.5 - 0.9 nm range. A large open aperture (30 x 20 (mm)) mica (002) spherically bent crystal with curvature radius R = 380 mm is used as dispersive and focusing element. The imaging plate is employed to obtain high spectral resolution with effective area of 30 x 80 (mm). The long designed path of the X-ray spectrometer beam is 980 mm from the source to the detector via the crystal. Experiment is carried out at a 20-J laser facility. X-ray spectra in an absolute intensity scale is obtained from Al laser produced plasmas created by laser energy of 6.78 J. Samples of spectra obtained with spectral resolution of up to E/鈻矱 ~ 1500 are presented. The results clearly show that the device is good to diagnose laser high-density plasmas.

  15. Crystal-field and covalency effects in uranates: an X-ray spectroscopic study

    Energy Technology Data Exchange (ETDEWEB)

    Butorin, Sergei M. [Molecular and Condensed Matter Physics, Department of Physics and Astronomy, Uppsala University, Uppsala (Sweden); Kvashnina, Kristina O. [European Synchrotron Radiation Facility, CS40220, Grenoble (France); Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Institute of Resource Ecology, Dresden (Germany); Smith, Anna L. [Department of Radiation Science and Technology, TU Delft (Netherlands); Popa, Karin [European Commission, Joint Research Centre, Institute for Transuranium Elements, Karlsruhe (Germany); Martin, Philippe M. [CEA Marcoule, CEA, DEN, DTEC/SECA/LCC, Bagnols-sur-Ceze (France)

    2016-07-04

    The electronic structure of U{sup V}- and U{sup VI}-containing uranates NaUO{sub 3} and Pb{sub 3}UO{sub 6} was studied by using an advanced technique, namely X-ray absorption spectroscopy (XAS) in high-energy-resolution fluorescence-detection (HERFD) mode. Due to a significant reduction in core-hole lifetime broadening, the crystal-field splittings of the 5f shell were probed directly in HERFD-XAS spectra collected at the U 3d edge, which is not possible by using conventional XAS. In addition, the charge-transfer satellites that result from U 5f-O 2p hybridization were clearly resolved. The crystal-field parameters, 5f occupancy, and degree of covalency of the chemical bonding in these uranates were estimated by using the Anderson impurity model by calculating the U 3d HERFD-XAS, conventional XAS, core-to-core (U 4f-3d transitions) resonant inelastic X-ray scattering (RIXS), and U 4f X-ray photoelectron spectra. The crystal field was found to be strong in these systems and the 5f occupancy was determined to be 1.32 and 0.84 electrons in the ground state for NaUO{sub 3} and Pb{sub 3}UO{sub 6}, respectively, which indicates a significant covalent character for these compounds. (copyright 2016 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  16. In vacuo X-ray data collection from graphene-wrapped protein crystals

    Energy Technology Data Exchange (ETDEWEB)

    Warren, Anna J. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); Crawshaw, Adam D. [Newcastle University, Newcastle upon Tyne NE2 4HH (United Kingdom); Trincao, Jose; Aller, Pierre; Alcock, Simon; Nistea, Ioana [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); Salgado, Paula S. [Newcastle University, Newcastle upon Tyne NE2 4HH (United Kingdom); Evans, Gwyndaf, E-mail: gwyndaf.evans@diamond.ac.uk [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom)

    2015-09-26

    A method is reported for collecting room-temperature data from protein crystals under vacuum by protecting them with a thin graphene layer. The measurement of diffraction data from macromolecular crystal samples held in vacuo holds the promise of a very low X-ray background and zero absorption of incident and scattered beams, leading to better data and the potential for accessing very long X-ray wavelengths (>3 Å) for native sulfur phasing. Maintaining the hydration of protein crystals under vacuum is achieved by the use of liquid jets, as with serial data collection at free-electron lasers, or is side-stepped by cryocooling the samples, as implemented at new synchrotron beamlines. Graphene has been shown to protect crystals from dehydration by creating an extremely thin layer that is impermeable to any exchanges with the environment. Furthermore, owing to its hydrophobicity, most of the aqueous solution surrounding the crystal is excluded during sample preparation, thus eliminating most of the background caused by liquid. Here, it is shown that high-quality data can be recorded at room temperature from graphene-wrapped protein crystals in a rough vacuum. Furthermore, it was observed that graphene protects crystals exposed to different relative humidities and a chemically harsh environment.

  17. Focused beam total reflection X-ray fluorescence with low power sources coupled to doubly curved crystal optics

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Z.W. [X-ray Optical Systems, Inc. East Greenbush, NY 12061 (United States)]. E-mail: zchen@xos.com; Mail, N. [Center For X-ray Optics, State University of New York, University at Albany (United States); Wei, F.Z. [X-ray Optical Systems, Inc. East Greenbush, NY 12061 (United States); MacDonald, C.A. [Center For X-ray Optics, State University of New York, University at Albany (United States); Gibson, W.M. [X-ray Optical Systems, Inc. East Greenbush, NY 12061 (United States)

    2005-04-30

    A focused beam total X-ray fluorescence technique was developed based on doubly curved crystal optics. This technique provides good detection sensitivity and spatial resolution for localized detection of surface deposits. Compact low power X-ray sources were used to demonstrate the benefit of the X-ray optics for focusing Cr K{alpha}, Cu K{alpha} and Mo K{alpha} radiation. The detection capability of the focused beam Total reflection X-ray fluorescence system was investigated with dried droplets of calibrated low concentration solutions. Detection limits at the femtogram level were demonstrated.

  18. Organic semiconducting single crystals as next generation of low-cost, room-temperature electrical X-ray detectors.

    Science.gov (United States)

    Fraboni, Beatrice; Ciavatti, Andrea; Merlo, Francesco; Pasquini, Luca; Cavallini, Anna; Quaranta, Alberto; Bonfiglio, Annalisa; Fraleoni-Morgera, Alessandro

    2012-05-02

    Direct, solid-state X-ray detectors based on organic single crystals are shown to operate at room temperature, in air, and at voltages as low as a few volts, delivering a stable and reproducible linear response to increasing X-ray dose rates, with notable radiation hardness and resistance to aging. All-organic and optically transparent devices are reported.

  19. Insights into the mechanism of X-ray-induced disulfide-bond cleavage in lysozyme crystals based on EPR, optical absorption and X-ray diffraction studies

    Energy Technology Data Exchange (ETDEWEB)

    Sutton, Kristin A. [Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14086 (United States); Black, Paul J.; Mercer, Kermit R. [University of Rochester Medical Center, Rochester, NY 14642 (United States); Garman, Elspeth F. [University of Oxford, South Parks Road, Oxford, Oxfordshire OX1 3QU (United Kingdom); Owen, Robin L. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Snell, Edward H., E-mail: esnell@hwi.buffalo.edu [Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14086 (United States); SUNY Buffalo Medical School, 700 Ellicott Street, Buffalo, NY 14203 (United States); Bernhard, William A. [University of Rochester Medical Center, Rochester, NY 14642 (United States); Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14086 (United States)

    2013-12-01

    Electron paramagnetic resonance (EPR) and online UV–visible absorption microspectrophotometry with X-ray crystallography have been used in a complementary manner to follow X-ray-induced disulfide-bond cleavage, to confirm a multi-track radiation-damage process and to develop a model of that process. Electron paramagnetic resonance (EPR) and online UV–visible absorption microspectrophotometry with X-ray crystallography have been used in a complementary manner to follow X-ray-induced disulfide-bond cleavage. Online UV–visible spectroscopy showed that upon X-irradiation, disulfide radicalization appeared to saturate at an absorbed dose of approximately 0.5–0.8 MGy, in contrast to the saturating dose of ∼0.2 MGy observed using EPR at much lower dose rates. The observations suggest that a multi-track model involving product formation owing to the interaction of two separate tracks is a valid model for radiation damage in protein crystals. The saturation levels are remarkably consistent given the widely different experimental parameters and the range of total absorbed doses studied. The results indicate that even at the lowest doses used for structural investigations disulfide bonds are already radicalized. Multi-track considerations offer the first step in a comprehensive model of radiation damage that could potentially lead to a combined computational and experimental approach to identifying when damage is likely to be present, to quantitate it and to provide the ability to recover the native unperturbed structure.

  20. Curved crystal spectrometer for the measurement of X-ray lines from laser-produced plasmas

    Institute of Scientific and Technical Information of China (English)

    SHI Jun; XIAO Sha-li; WANG Hong-jian; TANG Chang-huan; LIU Shen-ye

    2008-01-01

    In order to diagnose the laser-produced plasmas, a focusing curved crystal spectrometer has been developed for measuring the X-ray lines radiated from a laser-produced plasmas. The design is based on the fact that the ray emitted from a source located at one focus of an ellipse will converge on the other focus by the reflection of the elliptical surface. The focal length and the eccentricity of the ellipse are 1350 mm and 0.9586, respectively. The spectrometer can be used to measure the X-ray lines in the wavelength range of 0.2-0.37 nm, and a LiF crystal (200) (2d = 0.4027 nm) is used as dispersive element covering Bragg angle from 30° to 67.5°. The spectrometer was tested on Shenguang-Ⅱ which can deliver laser energy of 60-80 J/pulse and the laser wavelength is 0.35 μm. Photographs of spectra including the 1s2p 1p1-1s2 1S0 resonance line(w),the 1s2p 3P2-1s2 1S0 magnetic quadrupole line(x), the 1s2p 3p1 1s2 1S0 intercombination lines(y), the 1s2p 3S1-1s2 1S0 forbidden line(z) in helium-like Ti X XI and the 1s2s2p 2P3/2-1s22s 2S1/2 line(q) in lithium-like Ti X X have been recorded with a X-ray CCD camera. The experimental result shows that the wavelength resolution(λ/△λ) is above 1000 and the elliptical crystal spectrometer is suitable for X-ray spectroscopy.

  1. New structural studies of liquid crystal by reflectivity and resonant X-ray diffraction; Nouvelles etudes structurales de cristaux liquides par reflectivite et diffraction resonante des rayons X

    Energy Technology Data Exchange (ETDEWEB)

    Fernandes, P

    2007-04-15

    This memory presents three structural studies of smectic Liquid Crystals by reflectivity and resonant diffraction of X-rays. It is divided in five chapters. In the first a short introduction to Liquid Crystals is given. In particular, the smectic phases that are the object of this study are presented. The second chapter is consecrated to the X-ray experimental techniques that were used in this work. The three last chapters present the works on which this thesis can be divided. Chapter three demonstrates on free-standing films of MHPOBC (historic liquid crystal that possesses the antiferroelectric sub-phases) the possibility to extend the technique of resonant X-ray diffraction to liquid crystals without resonant element. In the fourth chapter the structure of the B{sub 2} liquid crystal phase of bent-core molecules (or banana molecules) is elucidated by using resonant X-ray diffraction combined with polarization analysis of the diffracted beam. A model of the polarization of the resonant beam diffracted by four different structures proposed for the B{sub 2} phase is developed in this chapter. In the fifth chapter a smectic binary mixture presenting a very original critical point of phase separation is studied by X-ray reflectivity and optical microscopy. A concentration gradient in the direction perpendicular to the plane of the film seems to be induced by the free-standing film geometry. The results of a simplified model of the system are compatible with this interpretation.

  2. Crystallization and X-ray diffraction studies of glutathione S-transferase from Escherichia coli

    Science.gov (United States)

    Nishida, Motohiko; Harada, Shigeharu; Satow, Yoshinori; Inoue, Hideshi; Takahashi, Kenji

    1996-10-01

    Crystals of glutathione S-transferase from Escherichia coli have been obtained by use of polyethylene glycol 6000 as a precipitant. The crystallization was performed in the presence of a glutathione sulfonate inhibitor under the acidic condition, with combination of the sitting-drop vapour-diffusion and the macro-seeding procedures. The crystals are of a thin-plate shape with typical sizes of 1.0 × 0.5 × 0.1 mm, and are stable against X-ray irradiation. They belong to the space group P2 12 12 1 with cell parameters of a = 90.47 Å, b = 93.87 Å and c = 51.10 Å, and diffract X-rays at least up to 2.3 Å resolution. The solvent content is 48% in volume, when a homodimeric molecule of the enzyme is assumed to occupy an asymmetric unit of the crystal. The crystals are suitable for three-dimensional structural studies. Diffraction data of the native crystal have been collected.

  3. X-ray absorption spectroscopy investigation of structurally modified lithium niobate crystals

    Energy Technology Data Exchange (ETDEWEB)

    Vitova, Tonya

    2008-02-15

    The type and concentration of impurity centers in different valence states are crucial for tuning the photorefractive properties of doped Lithium Niobate (LN) crystals. X-ray Absorption Spectroscopy (XAS) is an appropriate tool for studying the local structure of impurity centers. XAS combined with absorption in UV/VIS/IR and High Resolution X-ray Emission Spectroscopy (HRXES) provide information about the valence state of the dopant ions in as-grown, reduced or oxidized doped LN crystals. Cu (Cu{sup 1+} and Cu{sup 2+}) and Fe (Fe{sup 2+} and Fe{sup 3+}) atoms are found in two different valence states, whereas there are indications for a third Mn valency, in addition to Mn{sup 2+} and Mn{sup 3+} in manganese-doped LN crystals. One of the charge compensation mechanisms during reduction of copper- doped LN crystals is outgassing of oxygen atoms. Cu ions in the reduced crystals have at least two different site symmetries: twofold (Cu{sup 1+}) and sixfold (Cu{sup 2+}) coordinated by O atoms. Fe and Mn atoms are coordinated by six O atoms. Cu and Fe ions are found to occupy only Li sites, whereas Mn ions are also incorporated into Li and Nb sites. The refractive index change in LN crystals irradiated with {sup 3}He{sup 2+} ions is caused by structurally disordered centers, where Nb atoms are displaced from normal crystallographic sites and Li or/and O vacancies are present. (orig.)

  4. Crystallization and preliminary X-ray data of the FadA adhesin from Fusobacterium nucleatum

    Energy Technology Data Exchange (ETDEWEB)

    Nithianantham, Stanley [Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4935 (United States); Xu, Minghua [Department of Biological Sciences, School of Dentistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106-4905 (United States); Wu, Nan [Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4935 (United States); Han, Yiping W., E-mail: ywh2@case.edu [Department of Biological Sciences, School of Dentistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106-4905 (United States); Department of Pathology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106 (United States); Shoham, Menachem, E-mail: ywh2@case.edu [Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4935 (United States)

    2006-12-01

    The FadA adhesin from F. nucleatum, which is involved in bacterial attachment and invasion of human oral epithelial cells, has been crystallized in space group P6{sub 1} or P6{sub 5}, and X-ray data have been collected to 1.9 Å resolution. Fusobacterium nucleatum is a Gram-negative anaerobe prevalent in the oral cavity that is associated with periodontal disease, preterm birth and infections in other parts of the human body. The bacteria attach to and invade epithelial and endothelial cells in the gum tissue and elsewhere via a 13.7 kDa adhesin protein FadA (Fusobacterium adhesin A). FadA exists in two forms: the intact form (pre-FadA), consisting of 129 amino acids, and the mature form (mFadA), which lacks an 18-residue signal sequence. Both forms have been expressed in Escherichia coli and purified. mFadA has been crystallized. The crystals belong to the hexagonal space group P6{sub 1} or P6{sub 5}, with unit-cell parameters a = b = 59.3, c = 125.7 Å and one molecule per asymmetric unit. The crystals exhibit an unusually high solvent content of 74%. Synchrotron X-ray data have been collected to 1.9 Å. The crystals are suitable for X-ray structure determination. The crystal structure of FadA may provide a basis for the development of therapeutic agents to combat periodontal disease and other infections associated with F. nucleatum.

  5. Disordered crystal structure of pentamethylcyclopentadienylsodium as seen by high-resolution X-ray powder diffraction.

    Science.gov (United States)

    Tedesco, C; Dinnebier, R E; Olbrich, F; van Smaalen, S

    2001-10-01

    The crystal structure of pentamethylcyclopentadienylsodium, [NaC10H15] (NaCp*), has been determined from high-resolution X-ray powder diffraction. The compound crystallizes in space group Cmcm with lattice parameters a = 4.61030 (3), b = 16.4621 (3), c = 14.6751 (2) A, V = 1113.77 (4) A(3) (Z = 4). NaCp* forms polymeric multidecker chains along the a axis. The Rietveld refinement (R(p) = 0.050 and R(F) = 0.163) shows that the Cp* moieties occupy, with disorder, two different orientations rotated away from the eclipsed conformation by +/-13.8 degrees.

  6. Crystallization and preliminary X-ray crystallographic study of disproportionating enzyme from potato.

    Science.gov (United States)

    Imamura, Kayo; Matsuura, Takanori; Ye, Zhengmao; Takaha, Takeshi; Fujii, Kazutoshi; Kusunoki, Masami; Nitta, Yasunori

    2005-01-01

    Disproportionating enzyme (D-enzyme; EC 2.4.1.25) is a 59 kDa protein that belongs to the alpha-amylase family. D-enzyme catalyses intramolecular and intermolecular transglycosylation reactions of alpha-1,4 glucan. A crystal of the D-enzyme from potato was obtained by the hanging-drop vapour-diffusion method. Preliminary X-ray data showed that the crystal diffracts to 2.0 A resolution and belongs to space group C222(1), with unit-cell parameters a = 69.7, b = 120.3, c = 174.2 A.

  7. Evaluation of undoped ZnS single crystal materials for x-ray imaging applications

    Science.gov (United States)

    Saleh, Muad; Lynn, Kelvin G.; McCloy, John S.

    2017-05-01

    ZnS-based materials have a long history of use as x-ray luminescent materials. ZnS was one of the first discovered scintillators and is reported to have one of the highest scintillator efficiencies. The use of ZnS for high energy luminescence has been thus far limited to thin powder screens, such as ZnS:Ag which is used for detecting alpha radiation, due to opacity to its scintillation light, primarily due to scattering. ZnS in bulk form (chemical vapor deposited, powder processed, and single crystal) has high transmission and low scattering compared to powder screens. In this paper, the performance of single crystalline ZnS is evaluated for low energy x-ray (decay time, and low levels of afterglow. We present a trade study which compares the calculated scintillation gain and absolute efficiency for low energy x-rays (<10 keV) comparing thin (<100 μm) ZnS to CsI:Tl, Bi4Ge3O12 (BGO), and Y3Al5O12:Ce (YAG:Ce). The study also gives insight into the spatial resolution of these scintillators. Further, photoluminescence (PL) and PL excitation (PLE) of several undoped ZnS single crystals is compared to their Radioluminescence (RL) spectra. It was found that the ZnS emission wavelength varies on the excitation source energy.

  8. Mass Spectrometry Guided In Situ Proteolysis to Obtain Crystals for X-ray Structure Determination

    Energy Technology Data Exchange (ETDEWEB)

    Gheyi, Tarun; Rodgers, Logan; Romero, Richard; Sauder, J. Michael; Burley, Stephen K. (Lilly)

    2012-04-30

    A strategy for increasing the efficiency of protein crystallization/structure determination with mass spectrometry has been developed. This approach combines insights from limited proteolysis/mass spectrometry and crystallization via in situ proteolysis. The procedure seeks to identify protease-resistant polypeptide chain segments from purified proteins on the time-scale of crystal formation, and subsequently crystallizing the target protein in the presence of the optimal protease at the right relative concentration. We report our experience with 10 proteins of unknown structure, two of which yielded high-resolution X-ray structures. The advantage of this approach comes from its ability to select only those structure determination candidates that are likely to benefit from application of in situ proteolysis, using conditions most likely to result in formation of a stable proteolytic digestion product suitable for crystallization.

  9. IPC two-color analysis of x ray galaxy clusters

    Science.gov (United States)

    White, Raymond E., III

    1990-01-01

    The mass distributions were determined of several clusters of galaxies by using X ray surface brightness data from the Einstein Observatory Imaging Proportional Counter (IPC). Determining cluster mass distributions is important for constraining the nature of the dark matter which dominates the mass of galaxies, galaxy clusters, and the Universe. Galaxy clusters are permeated with hot gas in hydrostatic equilibrium with the gravitational potentials of the clusters. Cluster mass distributions can be determined from x ray observations of cluster gas by using the equation of hydrostatic equilibrium and knowledge of the density and temperature structure of the gas. The x ray surface brightness at some distance from the cluster is the result of the volume x ray emissivity being integrated along the line of sight in the cluster.

  10. Redetermination of Dy3Ni from single-crystal X-ray data

    Science.gov (United States)

    Levytskyy, Volodymyr; Babizhetskyy, Volodymyr; Kotur, Bohdan; Smetana, Volodymyr

    2013-01-01

    The classification of the title compound, tridysprosium nickel, into the Fe3C (or Al3Ni) structure type has been deduced from powder X-ray diffraction data with lattice parameters reported in a previous study [Lemaire & Paccard (1967 ▶). Bull. Soc. Fr. Mineral. Cristallogr. 40, 311–315]. The current re-investigation of Dy3Ni based on single-crystal X-ray data revealed atomic positional parameters and anisotropic displacement parameters with high precision. The asymmetric unit consists of two Dy and one Ni atoms. One Dy atom has site symmetry .m. (Wyckoff position 4c) and is surrounded by twelve Dy and three Ni atoms. The other Dy atom (site symmetry 1, 8d) has eleven Dy and three Ni atoms as neighbours, forming a distorted Frank–Kasper polyhedron. The coordination polyhedron of the Ni atom (.m., 4c) is a tricapped trigonal prism formed by nine Dy atoms. PMID:24454015

  11. Redetermination of Dy3Ni from single-crystal X-ray data

    Directory of Open Access Journals (Sweden)

    Volodymyr Levytskyy

    2013-11-01

    Full Text Available The classification of the title compound, tridysprosium nickel, into the Fe3C (or Al3Ni structure type has been deduced from powder X-ray diffraction data with lattice parameters reported in a previous study [Lemaire & Paccard (1967. Bull. Soc. Fr. Mineral. Cristallogr. 40, 311–315]. The current re-investigation of Dy3Ni based on single-crystal X-ray data revealed atomic positional parameters and anisotropic displacement parameters with high precision. The asymmetric unit consists of two Dy and one Ni atoms. One Dy atom has site symmetry .m. (Wyckoff position 4c and is surrounded by twelve Dy and three Ni atoms. The other Dy atom (site symmetry 1, 8d has eleven Dy and three Ni atoms as neighbours, forming a distorted Frank–Kasper polyhedron. The coordination polyhedron of the Ni atom (.m., 4c is a tricapped trigonal prism formed by nine Dy atoms.

  12. Redetermination of Ba2CdTe3 from single-crystal X-ray data

    Directory of Open Access Journals (Sweden)

    Min Yang

    2012-10-01

    Full Text Available The previous structure determination of the title compound, dibarium tritelluridocadmate, was based on powder X-ray diffraction data [Wang & DiSalvo (1999. J. Solid State Chem. 148, 464–467]. In the current redetermination from single-crystal X-ray data, all atoms were refined with anisotropic displacement parameters. The previous structure report is generally confirmed, but with some differences in bond lengths. Ba2CdTe3 is isotypic with Ba2MX3 (M = Mn, Cd; X = S, Se and features 1∞[CdTe2/2Te2/1]4− chains of corner-sharing CdTe4 tetrahedra running parallel [010]. The two Ba2+ cations are located between the chains, both within distorted monocapped trigonal–prismatic coordination polyhedra. All atoms in the structure are located on a mirror plane.

  13. Monoalkylated barbiturate derivatives: X-ray crystal structure, theoretical studies, and biological activities

    Science.gov (United States)

    Barakat, Assem; Al-Majid, Abdullah Mohammed; Soliman, Saied M.; Islam, Mohammad Shahidul; Ghawas, Hussain Mansur; Yousuf, Sammer; Choudhary, M. Iqbal; Wadood, Abdul

    2017-08-01

    Barbiturate derivatives are privileged structures with a broad range of pharmaceutical applications. We prepared a series of 5-monoalkylated barbiturate derivatives (3a-l) and evaluated, in vitro, their antioxidant (DPPH assay), and α-glucosidase inhibitory activities. Compounds 3a-l were synthesized via Michael addition. The structure of compound 3k was determined using X-ray single-crystal diffraction, and geometric parameters were calculated using density functional theory at the B3LYP/6-311G(d,p) level of theory. Further, the structural analysis of 3k were also investigated. Biological studies revealed that compounds 3b (IC50 = 133.1 ± 3.2 μM), 3d (IC50 = 305 ± 7.7 μM), and 3e (IC50 = 184 ± 2.3 μM) have potent α-glucosidase enzyme inhibitors and showed greater activity than the standard drug acarbose (IC50 = 841 ± 1.73 μM). Compounds 3a-3i were found to show weak antioxidant activity against 1,1-diphenyl-2-picryl-hydrazyl (DPPH) radicals (IC50 = 91 ± 0.75 to 122 ± 1.0 μM) when tested against a standard antioxidant, gallic acid (IC50 = 23 ± 0.43 μM).

  14. Water analysis via portable X-ray fluorescence spectrometry

    Science.gov (United States)

    Pearson, Delaina; Chakraborty, Somsubhra; Duda, Bogdan; Li, Bin; Weindorf, David C.; Deb, Shovik; Brevik, Eric; Ray, D. P.

    2017-01-01

    Rapid, in-situ elemental water analysis would be an invaluable tool in studying polluted and/or salt-impacted waters. Analysis of water salinity has commonly used electrical conductance (EC); however, the identity of the elements responsible for the salinity are not revealed using EC. Several studies have established the viability of using portable X-ray fluorescence (PXRF) spectrometry for elemental data analysis of soil, sediment, and other matrices. However, the accuracy of PXRF is known to be affected while scanning moisture-laden soil samples. This study used PXRF elemental data in water samples to predict water EC. A total of 256 water samples, from 10 different countries were collected and analyzed via PXRF, inductively coupled plasma atomic emission spectroscopy (ICP-AES), and a digital salinity bridge. The PXRF detected some elements more effectively than others, but overall results indicated that PXRF can successfully predict water EC via quantifying Cl in water samples (validation R2 and RMSE of 0.77 and 0.95 log μS cm-1, respectively). The findings of this study elucidated the potential of PXRF for future analysis of pollutant and/or metal contaminated waters.

  15. Native MS and ECD Characterization of a Fab-Antigen Complex May Facilitate Crystallization for X-ray Diffraction

    Science.gov (United States)

    Zhang, Ying; Cui, Weidong; Wecksler, Aaron T.; Zhang, Hao; Molina, Patricia; Deperalta, Galahad; Gross, Michael L.

    2016-07-01

    Native mass spectrometry (MS) and top-down electron-capture dissociation (ECD) combine as a powerful approach for characterizing large proteins and protein assemblies. Here, we report their use to study an antibody Fab (Fab-1)-VEGF complex in its near-native state. Native ESI with analysis by FTICR mass spectrometry confirms that VEGF is a dimer in solution and that its complex with Fab-1 has a binding stoichiometry of 2:2. Applying combinations of collisionally activated dissociation (CAD), ECD, and infrared multiphoton dissociation (IRMPD) allows identification of flexible regions of the complex, potentially serving as a guide for crystallization and X-ray diffraction analysis.

  16. Recombinant expression, purification, crystallization and preliminary X-ray diffraction analysis of the C-terminal DUF490(963-1138) domain of TamB from Escherichia coli.

    Science.gov (United States)

    Josts, Inokentijs; Grinter, Rhys; Kelly, Sharon M; Mosbahi, Khedidja; Roszak, Aleksander; Cogdell, Richard; Smith, Brian O; Byron, Olwyn; Walker, Daniel

    2014-09-01

    TamB is a recently described inner membrane protein that, together with its partner protein TamA, is required for the efficient secretion of a subset of autotransporter proteins in Gram-negative bacteria. In this study, the C-terminal DUF490963-1138 domain of TamB was overexpressed in Escherichia coli K-12, purified and crystallized using the sitting-drop vapour-diffusion method. The crystals belonged to the primitive trigonal space group P3121, with unit-cell parameters a = b = 57.34, c = 220.74 Å, and diffracted to 2.1 Å resolution. Preliminary secondary-structure and X-ray diffraction analyses are reported. Two molecules are predicted to be present in the asymmetric unit. Experimental phasing using selenomethionine-labelled protein will be undertaken in the future.

  17. Evaluation of the Quality of Sapphire Using X-Ray Rocking Curves and Double-Crystal X-Ray Topography

    Science.gov (United States)

    1994-05-01

    hard, high-strength, chemically resistant optical windows; and sub- srates for the growth of epitaxial films. The quality of a sapphire crystal can... crystal diffractometer. Single- crystal sapphire may be grown by a variety of different methods, of which the more common are Verneuil (flame fusion...Linear features (L), which may represent slight variations in lattice parameter along the crystal growth front, or dislocation networks, ad small

  18. Single-crystal X-ray diffraction studies of photo-induced molecular species.

    Science.gov (United States)

    Cole, Jacqueline M

    2004-10-20

    This tutorial review gathers together the recent developments in single-crystal X-ray diffraction that are starting to enable one to quantify directly the nature of light-induced electronic perturbations in chemical structures. Such structural information is key to understanding many photo-activated chemical processes and physical properties, and a description of the scientific impetus behind this incipient area of structural science, from academic and industrial perspectives, is given. Photoisomerism processes, solid-state photochemical reactions and spin-cross-over magnetic transitions, that have long-lived or irreversible light-induced states, are best understood by unravelling their three-dimensional structures measured in situ in their photo-converted state. A review of steady-state laser-induced single-crystal X-ray diffraction studies conducted, to date, and the experimental methodologies used in order to realise such structures, is presented. The structural characterisation of more transient photo-induced species (down to picosecond lifetimes) is paramount to a better understanding of the materials that undergo high-speed electronic switching, which make operative much of the electronics and optics industry, since there exists an inherent relationship between the excited-state structure and the physical properties exhibited. Prime examples include excited-state structures of molecular conductors and luminescent materials with potential applications as molecular wires, light-emitting diodes, non-linear optics, triboluminescence and electroluminescence. Previously, only indirect and qualitative interpretations of the nature of these excited-states could be formulated via spectroscopic techniques, but the developments in ms-ps time-resolved laser pump, X-ray probe single-crystal diffraction techniques, described herein, are overcoming this barrier, affording results that are entirely quantitative via a three-dimensional structural representation. In this

  19. Development of low-energy x-ray fluorescence micro-distribution analysis using a laser plasma x-ray source and multilayer optics?

    NARCIS (Netherlands)

    Stuik, R.; Shmaenok, L. A.; Fledderus, H.; Andreev, S. S.; Shamov, E. A.; Zuev, S. Y.; Salashchenko, N. N.; F. Bijkerk,

    1999-01-01

    A new technique is presented for low-energy X-ray fluorescence micro-distribution analysis of low-Z elements at micrometer spatial resolutions. The technique is based on the use of a laser plasma X-ray source and spherically curved multilayer optics. A large collimator is used to focus the light fro

  20. ANALYSIS OF EQUIPMENT PROVISIONS FOR X-RAY DIAGNOSTICS IN THE RUSSIAN FEDERATION

    Directory of Open Access Journals (Sweden)

    N. M. Vishnyakova

    2010-01-01

    Full Text Available Analysis of equipment provisions for X-ray diagnostics in the Russian Federation for the period from 2000 to 2006 is being presented. The article records the lag of Russia behind the countries with high level of public health service development both for total amount of X-ray diagnostic equipment and for the rate of their amount growth. The lag of national X-ray diagnostic equipment is especially high for the equipment for special X-ray examinations. Half of all X-ray equipment in Russia has a life time of 10 and more years. Equipment for the standard X-ray examinations prevails in its structure in contrast to the countries with high level of public health service. More than one third of equipment for fluoroscopy is not equipped with amplifiers of X-ray image. The share of digital X-ray diagnostic equipment for standard X-ray examinations is 5%, while in the economically developed countries mainly digital technologies are applied. Significant differences in the quantitative and qualitative aspects of current state of X-ray diagnostic equipment in the various Federal districts and administrative territories of the Russian Federation are observed.

  1. Tunable hard X-ray spectrometer utilizing asymmetric planes of a quartz transmission crystal.

    Science.gov (United States)

    Seely, John F; Henins, Albert; Feldman, Uri

    2016-05-01

    A Cauchois type hard x-ray spectrometer was developed that utilizes the (301) diffraction planes at an asymmetric angle of 23.51° to the normal to the surface of a cylindrically curved quartz transmission crystal. The energy coverage is tunable by rotating the crystal and the detector arm, and spectra were recorded in the 8 keV to 20 keV range with greater than 2000 resolving power. The high resolution results from low aberrations enabled by the nearly perpendicular angle of the diffracted rays with the back surface of the crystal. By using other asymmetric planes of the same crystal and rotating to selected angles, the spectrometer can operate with high resolution up to 50 keV.

  2. Synthesis and X-ray Crystal Structure of a New Molecular Clip

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The synthesis and X-ray crystal structure of a new molecular clip 2 was reported.It (C24H24N4O2, Mr = 400.47) crystallizes in the space group C2/c with a = 15.587(2), b =8.5805(12), c = 15.259(2)(A),β= 102.448(3)°, V = 1992.9 (5)(A)3, Z= 4, Dc = 1.335 g/cm3,μ= 0.087mm-1 and F(000) = 848.It remains monomeric in the crystal and a tape-like structure is formed in the crystal structure of molecular clip.The most unusual structural feature of 2 is the boat conformation of its cyclohexyl ring imposed by the ring fusion at C(9)-C(9a).

  3. Purification, crystallization, and preliminary X-ray diffraction study of purine nucleoside phosphorylase from E. coli

    Science.gov (United States)

    Abramchik, Yu. A.; Timofeev, V. I.; Zhukhlistova, N. E.; Muravieva, T. I.; Esipov, R. S.; Kuranova, I. P.

    2015-07-01

    Crystals of E. coli purine nucleoside phosphorylase were grown in microgravity by the capillary counter-diffusion method through a gel layer. The X-ray diffraction data set suitable for the determination of the three-dimensional structure at atomic resolution was collected from one crystal at the Spring-8 synchrotron facility to 0.99 Å resolution. The crystals belong to sp. gr. P21 and have the following unit-cell parameters: a = 74.1 Å, b = 110.2 Å, c = 88.2 Å, α = γ = 90°, β = 111.08°. The crystal contains six subunits of the enzyme comprising a hexamer per asymmetric unit. The hexamer is the biological active form of E. coli. purine nucleoside phosphorylase.

  4. Purification, crystallization, and preliminary X-ray diffraction study of purine nucleoside phosphorylase from E. coli

    Energy Technology Data Exchange (ETDEWEB)

    Abramchik, Yu. A., E-mail: inna@ns.crys.ras.ru; Timofeev, V. I., E-mail: espiov@ibch.ru; Zhukhlistova, N. E., E-mail: tostars@mail.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation); Muravieva, T. I.; Esipov, R. S. [Russian Academy of Sciences, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry (Russian Federation); Kuranova, I. P. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2015-07-15

    Crystals of E. coli purine nucleoside phosphorylase were grown in microgravity by the capillary counter-diffusion method through a gel layer. The X-ray diffraction data set suitable for the determination of the three-dimensional structure at atomic resolution was collected from one crystal at the Spring-8 synchrotron facility to 0.99 Å resolution. The crystals belong to sp. gr. P2{sub 1} and have the following unit-cell parameters: a = 74.1 Å, b = 110.2 Å, c = 88.2 Å, α = γ = 90°, β = 111.08°. The crystal contains six subunits of the enzyme comprising a hexamer per asymmetric unit. The hexamer is the biological active form of E. coli. purine nucleoside phosphorylase.

  5. X-ray perfection study of Verneuil-grown SrTiO 3 crystals

    Science.gov (United States)

    Yoshimura, J.; Sakamoto, T.; Usui, S.; Kimura, S.

    1998-07-01

    Dislocations, subgrain textures and other long-range strains in Verneuil-grown SrTiO 3 crystals, used widely as a substrate for growing high- Tc superconducting thin films, have been studied by reflection and transmission X-ray topography to characterize the crystal in regard to structural perfection. It was found that dislocations are nearly aligned along the directions and most of them are of pure edge type, presumably as a property of annealed crystals with simple cubic lattice. This entire dislocation alignment causes a strong long-range distortion about the [0 0 1] axis in anisotropic (1 1 0)-oriented crystal plates. Burgers vectors both of and types were observed. It was also found that the surfaces of some samples were finished highly strain-free as well as optically flat by the mechanochemical polishing.

  6. X-ray photoelectron spectroscopy, high-resolution X-ray diffraction and refractive index analyses of Ti-doped lithium niobate (Ti:LiNbO3) nonlinear optical single crystal

    Indian Academy of Sciences (India)

    P Kumar; S Moorthy Babu; S Perero; Rajamaniccam L Sai; I Bhaumik; S Ganesamoorthy; A K Karnal

    2010-11-01

    Congruent LiNbO3 single crystals with Ti ion dopants (2 and 5 mol%) were successfully grown by Czochralski technique in the automatic diameter control facility. As-grown crystal boules were oriented into (0 0 1) direction cut and optically polished for all measurements. Influence of Ti-ion incorporation into LiNbO3 was studied by core level XPS analysis. Powder X-ray diffraction studies were carried out on doped lithium niobate for phase identification. High-resolution X-ray diffraction technique was used to study the crystalline quality through full-width at half-maximum values. The refractive index values are more for doped samples than for pure sample as determined by prism coupling technique with different laser sources.

  7. Revised stereochemistry of ceramide-trafficking inhibitor HPA-12 by X-ray crystallography analysis.

    Science.gov (United States)

    Ueno, Masaharu; Huang, Yi-Yong; Yamano, Akihito; Kobayashi, Shū

    2013-06-07

    In response to Berkeš's report revising the stereochemistry of HPA-12, an important ceramide-trafficking inhibitor that was discovered and synthesized and its stereochemistry determined in 2001, the synthesis and the stereochemistry were reinvestigated. A large-scale synthetic method for HPA-12 based on a Zn-catalyzed asymmetric Mannich-type reaction in water was developed. Single crystals of HPA-12 for X-ray crystallographic analysis were obtained from ethyl propionate/n-hexane, and the stereochemistry was definitely determined to be 1R,3S, consistent with Berkeš's revised structure.

  8. Normal incidence X-ray standing wave analysis of thin gold films

    Science.gov (United States)

    Satterley, Christopher J.; Lovelock, Kevin R. J.; Thom, Ian; Dhanak, Vinod R.; Buck, Manfred; Jones, Robert G.

    2006-11-01

    Normal incidence X-ray standing wave (NIXSW) analysis has been successfully performed on epitaxial gold films on mica substrates using reflection from the (1 1 1) planes parallel to the surface. We show that NIXSW can be used to monitor the decrease in order within the gold film caused by annealing, and the position of sulfur within a monolayer of methyl thiolate (CH 3S-) on the surface. The Au-S layer spacing was found to be 2.54 ± 0.05 Å, in close agreement with previous work on a single crystal system.

  9. Characterisation of vapour grown CdZnTe crystals using synchrotron X-ray topography

    Science.gov (United States)

    Egan, Christopher K.; Choubey, Ashutosh; Moore, Moreton; Cernik, Robert J.

    2012-03-01

    Synchrotron white beam X-ray topography has been used to characterise bulk crystal defects of thick vapour grown CdZnTe crystals. Whole 50 mm diameter wafers with thicknesses in the range of 2-3 mm were sliced from boules grown by the multi-tube physical vapour transport method and analysed by diffraction topography in a transmission geometry. A variety of defects were observed including cracks, voids and grain boundaries. The largest quantity of defects observed were sub-grains appearing as localised increased intensity in the topographs. The periphery of the wafers showed the highest number of defects, whereas central regions where largely defect-free. We failed to observe any inclusions or precipitates within these crystals. Surface damage from wire-saw cutting was also observed on poorly processed wafers; these defects were otherwise invisible to standard characterisation methods. X-ray topography has proven to be a useful tool for non-destructively investigating bulk extended defects in CdZnTe crystals for radiation detector applications.

  10. Mineral crystal alignment in mineralized fracture callus determined by 3D small-angle X-ray scattering

    Energy Technology Data Exchange (ETDEWEB)

    Liu Yifei; Manjubala, Inderchand; Fratzl, Peter [Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam (Germany); Roschger, Paul [4th Medical Department, Ludwig Boltzmann Institute of Osteology at Hanusch Hospital of WGKK and AUVA Trauma Centre Meidling, 1140 Vienna (Austria); Schell, Hanna; Duda, Georg N, E-mail: fratzl@mpikg.mpg.d [Julius Wolff Institut and Center for Musculoskeletal Surgery, Charite- University Medicine Berlin, Augustenburger Platz 1, 13353 Berlin (Germany)

    2010-10-01

    Callus tissue formed during bone fracture healing is a mixture of different tissue types as revealed by histological analysis. But the structural characteristics of mineral crystals within the healing callus are not well known. Since two-dimensional (2D) scanning small-angle X-ray scattering (sSAXS) patterns showed that the size and orientation of callus crystals vary both spatially and temporally [1] and 2D electron microscopic analysis implies an anisotropic property of the callus morphology, the mineral crystals within the callus are also expected to vary in size and orientation in 3D. Three-dimensional small-angle X-ray scattering (3D SAXS), which combines 2D SAXS patterns collected at different angles of sample tilting, has been previously applied to investigate bone minerals in horse radius [2] and oim/oim mouse femur/tibia [3]. We implement a similar 3D SAXS method but with a different way of data analysis to gather information on the mineral alignment in fracture callus. With the proposed accurate yet fast assessment of 3D SAXS information, it was shown that the plate shaped mineral particles in the healing callus were aligned in groups with their predominant orientations occurring as a fiber texture.

  11. Characterization of X-ray polycapillary optics by LiF crystal radiation detectors through confocal fluorescence microscopy

    Science.gov (United States)

    Bonfigli, Francesca; Hampai, Dariush; Dabagov, Sultan B.; Montereali, Rosa Maria

    2016-08-01

    Solid-state radiation imaging detectors based on photoluminescent colour centres in lithium fluoride (LiF) crystals have been successfully tested for both advanced 2D and 3D characterizations of X-ray polycapillary optics by a table-top laboratory system. Polycapillary optics can control X-ray beams propagation and allows obtaining quasi-parallel beam (half-lens) or focused beams (full-lens). The combination of a fine-focused micro X-ray tube and a polycapillary lens can provide the high intensity radiation fluxes that are necessary for high resolution X-ray imaging. In this paper we present novel results about advanced characterization of these complex optics by 2D as well as 3D confocal laser fluorescence microscopy of X-ray irradiated LiF crystal detectors. Two dimensional high spatial resolution images on a wide field of view of transmitted X-rays through a semi-lens and 3D direct inspection of the coloured volumes produced in LiF crystals by both focused and parallel X-ray beam transmitted by a full and a semi-lens, respectively, as well as their 3D reconstructions were obtained. The results show that the photoluminescent colour centres volume in LiF crystals combined with an optical sectioning reading system provide information about tomography of transmitted X-ray beams by policapillary optics in a single exposure process. For the first time, the use of LiF crystal plates as versatile radiation imaging luminescent detectors have been used to characterize the operation of polycapillary optics as X-ray lens, in focusing and parallel mode.

  12. Project Title: Radiochemical Analysis by High Sensitivity Dual-Optic Micro X-ray Fluorescence

    Energy Technology Data Exchange (ETDEWEB)

    Havrilla, George J.; Gao, Ning

    2003-06-01

    A novel dual-optic micro X-ray fluorescence instrument will be developed to do radiochemical analysis of high-level radioactive wastes at DOE sites such as Savannah River Site and Hanford. This concept incorporates new X-ray optical elements such as monolithic polycapillaries, which focus X-rays. The polycapillary optic can be used to focus X-rays emitted by the X-ray tube thereby increasing the X-ray flux on the sample over 1000 times. The polycapillary optic will also be used to collect the X-rays from the excitation site. This will effectively screen the radiation background from the radioactive species in the specimen. This dual-optic approach significantly reduces the background and increases the analyte signal thereby increasing the sensitivity of the analysis. This dual-capillary design is essentially a confocal (having the same foci) design, i.e. the detected X-rays are only emitted from the overlap of the two focal spots. This increases spatial resolution and reduce s background. The integration of the X-ray optics increases the signal-to-noise and thereby increases the sensitivity of the analysis for low-level analytes. This work will address a key need for radiochemical analysis of high-level waste using a non-destructive, multi-element, and rapid method in a radiation environment. There is significant potential that this instrumentation could be capable of on-line analysis for process waste stream characterization at DOE sites.

  13. Radiochemical Analysis by High Sensitivity Dual-Optic Micro X-ray Fluorescence

    Energy Technology Data Exchange (ETDEWEB)

    Havrilla, George J.; Gao, Ning

    2004-06-01

    A novel dual-optic micro X-ray fluorescence instrument will be developed to do radiochemical analysis of high-level radioactive wastes at DOE sites such as Savannah River Site and Hanford. This concept incorporates new X-ray optical elements such as monolithic polycapillaries, which focus X-rays. The polycapillary optic can be used to focus X-rays emitted by the X-ray tube thereby increasing the X-ray flux on the sample over 1000 times. The polycapillary optic will also be used to collect the X-rays from the excitation site. This will effectively screen the radiation background from the radioactive species in the specimen. This dual-optic approach significantly reduces the background and increases the analyte signal thereby increasing the sensitivity of the analysis. This dual-capillary design is essentially a confocal (having the same foci) design, i.e. the detected X-rays are only emitted from the overlap of the two focal spots. This increases spatial resolution and reduces background. The integration of the X-ray optics increases the signal-to-noise and thereby increases the sensitivity of the analysis for low-level analytes. This work will address a key need for radiochemical analysis of high-level waste using a non-destructive, multi-element, and rapid method in a radiation environment. There is significant potential that this instrumentation could be capable of on-line analysis for process waste stream characterization at DOE sites.

  14. Photonic Material Selection of Scintillation Crystals Using Monte Carlo Method for X-Ray Detection in Industrial Computed Tomography

    Directory of Open Access Journals (Sweden)

    Peng He

    2014-01-01

    Full Text Available Currently industrial X-CT system is designed according to characteristics of test objects, and test objects determine industrial X-CT system structure, X-ray detector/sensor property, scanning mode, and so forth. So there are no uniform standards for the geometry size of scintillation crystals of detector. Moreover, scintillation crystals are usually mixed with some highly toxic impurity elements, such as Tl and Cd. Thus, it is indispensable for establishing guidelines of engineering practice to simulate X-ray detection performances of different scintillation crystals. This paper focuses on how to achieve high efficient X-ray detection in industrial X-CT system which used Monte Carlo (MC method to study X-ray energy straggling characteristics, full energy peak efficiency, and conversion efficiency of some scintillation crystals (e.g., CsI(Tl, NaI(Tl, and CdWO4 after X-ray interacted with these scintillation crystals. Our experimental results demonstrate that CsI(Tl scintillation crystal has the advantages of conversion efficiency, spectral matching, manufacturing process, and full energy peak efficiency; it is an ideal choice for high efficient X-ray detection in industrial X-CT system.

  15. X-ray Imaging of MagLIF Experiments Using a Spherically-Bent Crystal Optic

    Science.gov (United States)

    Harding, E. C.; Gomez, M. R.; Jennings, C. A.; Knapp, P. F.; Slutz, S. A.; Sefkow, A. B.; Awe, T. J.; Hansen, S. B.; Peterson, K. J.; Hahn, K. D.; McBride, R. D.; Rochau, G. A.; Sinars, D. B.; Golovkin, I.

    2015-11-01

    The recent Magnetized Liner Inertial Fusion (MagLIF) experiments performed on Sandia's Z-machine produced significant thermonuclear DD fusion yields that were accompanied by observable x-ray emission [M.R. Gomez et. al., PRL (2014)]. The MagLIF experiments relied on a spherically-bent crystal optic to image portions of the x-ray continuum that were generated by the hot stagnation plasma. The images of stagnation show a long (6 to 8 mm) and narrow (~100 micron) column of x-ray emission with structure in both directions. This structure may be caused by variations in the electron temperature (Te) and density (ne) , as well as opacity variations in the surrounding Be pusher. Here we investigate the possible contributions from each of these effects. We will also discuss the development of a diagnostic technique in which Te and ne of the DD fuel are inferred from spectra emitted by Fe impurities that become ionized to a He-like charge state. Sandia National Labs is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. DoE NNSA under contract DE-AC04-94AL85000.

  16. Determination of Fe charge-state distributions in PLT by Bragg crystal x-ray spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Hill, K.W.; von Goeler, S.; Bitter, M.

    1978-08-01

    A curved-crystal Bragg x-ray spectrometer has been used to measure K..cap alpha.. or 1s-2p radiation from highly stripped Fe XVIII to Fe XXV impurity ions in the PLT tokamak. The spectrometer has sufficient energy resolution (approximately < 4 eV at 6400 eV) to distinguish between the different ionization states of iron by measuring the energy shift of the K..cap alpha.. x rays. The measured wavelengths agree well with theory and with spectra from solar flares and from laser-produced plasmas. The distribution of Fe charge states in the center of the discharge has been inferred from a comparison of the measured x-ray spectrum with theory. The shape of the spectrum depends strongly on electron temperature (T/sub e/) in the range T/sub e/ = 800 to 1500 eV. Within the factor of two uncertainty in L-shell ionization cross sections, measured intensities agree with theory, which is based on coronal equilibrium, indicating that the ion life-time in the center of the plasma is approximately equal to or greater than the equilibration time.

  17. Single crystal X-ray structure of the artists' pigment zinc yellow

    Science.gov (United States)

    Simonsen, Kim Pilkjær; Christiansen, Marie Bitsch; Vinum, Morten Gotthold; Sanyova, Jana; Bendix, Jesper

    2017-08-01

    The artists' pigment zinc yellow is in general described as a complex potassium zinc chromate with the empirical formula 4ZnCrO4·K2O·3H2O. Even though the pigment has been in use since the second half of the 19th century also in large-scale industrial applications, the exact structure had hitherto been unknown. In this work, zinc yellow was synthesised by precipitation from an aqueous solution of zinc nitrate and potassium chromate under both neutral and basic conditions, and the products were compared with the pigment used in industrial paints. Analyses by Raman microscopy (MRS), scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS), attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR), and powder X-ray diffraction (PXRD), showed that the synthesised products and the industrial pigment were identical. Single-crystal X-ray crystallography determined the structure of zinc yellow as KZn2(CrO4)2(H2O)(OH) or as KZn2(CrO4)2(H3O2) emphasizing the μ-H3O2- moiety. Notably, the zinc yellow is isostructural to the recently structurally characterized cadmium analog and both belong to the natrochalcite structure type.

  18. Synthesis, X-ray crystal structure, DNA binding and Nuclease activity of lanthanide(III) complexes of 2-benzoylpyridine acetylhydrazone

    Indian Academy of Sciences (India)

    KARREDDULA RAJA; AKKILI SUSEELAMMA; KATREDDI HUSSAIN REDDY

    2016-08-01

    Lanthanide(III) complexes of general formula [La(BPAH)₂(NO₃)₃] and [Ce(BPAH)₂(NO₃)(H₂O)₂] 2NO₃.H₂O (where, BPAH = 2-benzoylpyridine acetyl hydrazone), were synthesized and characterized by elemental analysis, molar conductance, IR spectroscopy and single crystal X-ray diffraction and Hirschfeld studies. The central metal ion is 12-coordinate in lanthanum complex and 10-coordinated in the cerium complex. The coordination polyhedra around the lanthanum and cerium were found to have distorted icosahedron and distorted bicapped square antiprism respectively. DNA binding and nuclease activity of these complexes were also investigated in the present work.

  19. X-ray CT analysis of pore structure in sand

    Science.gov (United States)

    Mukunoki, Toshifumi; Miyata, Yoshihisa; Mikami, Kazuaki; Shiota, Erika

    2016-06-01

    The development of microfocused X-ray computed tomography (CT) devices enables digital imaging analysis at the pore scale. The applications of these devices are diverse in soil mechanics, geotechnical and geoenvironmental engineering, petroleum engineering, and agricultural engineering. In particular, the imaging of the pore space in porous media has contributed to numerical simulations for single-phase and multiphase flows or contaminant transport through the pore structure as three-dimensional image data. These obtained results are affected by the pore diameter; therefore, it is necessary to verify the image preprocessing for the image analysis and to validate the pore diameters obtained from the CT image data. Moreover, it is meaningful to produce the physical parameters in a representative element volume (REV) and significant to define the dimension of the REV. This paper describes the underlying method of image processing and analysis and discusses the physical properties of Toyoura sand for the verification of the image analysis based on the definition of the REV. On the basis of the obtained verification results, a pore-diameter analysis can be conducted and validated by a comparison with the experimental work and image analysis. The pore diameter is deduced from Young-Laplace's law and a water retention test for the drainage process. The results from previous study and perforated-pore diameter originally proposed in this study, called the voxel-percolation method (VPM), are compared in this paper. In addition, the limitations of the REV, the definition of the pore diameter, and the effectiveness of the VPM for an assessment of the pore diameter are discussed.

  20. The XMM Cluster Survey: X-ray analysis methodology

    CERN Document Server

    Lloyd-Davies, E J; Hosmer, Mark; Mehrtens, Nicola; Davidson, Michael; Sabirli, Kivanc; Mann, Robert G; Hilton, Matt; Liddle, Andrew R; Viana, Pedro T P; Campbell, Heather C; Collins, Chris A; Dubois, E Naomi; Freeman, Peter; Hoyle, Ben; Kay, Scott T; Kuwertz, Emma; Miller, Christopher J; Nichol, Robert C; Sahlen, Martin; Stanford, S Adam; Stott, John P

    2010-01-01

    The XMM Cluster Survey (XCS) is a serendipitous search for galaxy clusters using all publicly available data in the XMM- Newton Science Archive. Its main aims are to measure cosmological parameters and trace the evolution of X-ray scaling relations. In this paper we describe the data processing methodology applied to the 5776 XMM observations used to construct the current XCS source catalogue. A total of 3669 > 4-{\\sigma} cluster candidates with >50 background-subtracted X-ray counts are extracted from a total non-overlapping area suitable for cluster searching of 410 deg^2 . Of these, 1022 candidates are detected with >300 X-ray counts, and we demonstrate that robust temperature measurements can be obtained down to this count limit. We describe in detail the automated pipelines used to perform the spectral and surface brightness fitting for these sources, as well as to estimate redshifts from the X-ray data alone. A total of 517 (126) X-ray temperatures to a typical accuracy of <40 (<10) per cent have ...