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Sample records for crystals diffracted x-rays

  1. 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

  2. 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.

  3. 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...

  4. 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.

  5. 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...

  6. X-Ray Diffraction.

    Science.gov (United States)

    Smith, D. K.; Smith, K. L.

    1980-01-01

    Reviews applications in research and analytical characterization of compounds and materials in the field of X-ray diffraction, emphasizing new developments in applications and instrumentation in both single crystal and powder diffraction. Cites 414 references. (CS)

  7. X-Ray Diffraction.

    Science.gov (United States)

    Smith, D. K.; Smith, K. L.

    1980-01-01

    Reviews applications in research and analytical characterization of compounds and materials in the field of X-ray diffraction, emphasizing new developments in applications and instrumentation in both single crystal and powder diffraction. Cites 414 references. (CS)

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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...

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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 ...

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  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. 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.

  17. 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...

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  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 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.

  7. Revisit of alpha-chitin crystal structure using high resolution X-ray diffraction data.

    Science.gov (United States)

    Sikorski, Pawel; Hori, Ritsuko; Wada, Masahisa

    2009-05-11

    High resolution synchrotron X-ray fiber diffraction data recorded from crab tendon chitin have been used to describe the crystal structure of alpha-chitin. Crystal structures at 100 and 300 K have been solved using restrained crystallographic refinement against diffraction intensities measured from the fiber diffraction patterns. The unit cell contains two polymer chains in a 2(1) helix conformation and in the antiparallel orientation. The best agreement between predicated and observed X-ray diffraction intensities is obtained for a model that includes two distinctive conformations of C6-O6 hydroxymethl group. Those conformations are different from what is proposed in the generally accepted alpha-chitin crystal structure (J. Mol. Biol. 1978, 120, 167-181). Based on refined positions of the O6 atoms, a network of hydrogen bonds involving O6 is proposed. This network of hydrogen bonds can explain the main features of the polarized FTIR spectra of alpha-chitin and sheds some light on the origin of splitting of the amide I band observed on alpha-chitin IR spectra.

  8. 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.

  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. 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.

  11. 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

  12. High resolution x-ray and gamma ray imaging using diffraction lenses with mechanically bent crystals

    Science.gov (United States)

    Smither, Robert K.

    2008-12-23

    A method for high spatial resolution imaging of a plurality of sources of x-ray and gamma-ray radiation is provided. High quality mechanically bent diffracting crystals of 0.1 mm radial width are used for focusing the radiation and directing the radiation to an array of detectors which is used for analyzing their addition to collect data as to the location of the source of radiation. A computer is used for converting the data to an image. The invention also provides for the use of a multi-component high resolution detector array and for narrow source and detector apertures.

  13. 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.

  14. 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.

  15. Crystallization and preliminary X-ray diffraction study of phosphoribosyl pyrophosphate synthetase from E. Coli

    Energy Technology Data Exchange (ETDEWEB)

    Timofeev, V. I., E-mail: inna@ns.crys.ras.ru; Abramchik, Yu. A., E-mail: tostars@mail.ru; Zhukhlistova, N. E., E-mail: ugama@yandex.ru; Kuranova, I. P. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2015-09-15

    Enzymes of the phosphoribosyl pyrophosphate synthetase family (PRPPS, EC 2.7.6.1) catalyze the formation of 5-phosphoribosyl pyrophosphate (5-PRPP) from adenosine triphosphate and ribose 5-phosphate. 5-Phosphoribosyl pyrophosphate is an important intermediate in the synthesis of purine, pyrimidine, and pyridine nucleotides, as well as of the amino acids histidine and tryptophan. The crystallization conditions for E. coli PRPPS were found by the vapor-diffusion technique and were optimized to apply the capillary counter-diffusion technique. The X-ray diffraction data set was collected from the crystals grown by the counter-diffusion technique using a synchrotron radiation source to 3.1-Å resolution. The crystals of PRPPS belong to sp. gr. P6{sub 3}22 and have the following unit-cell parameters: a = b = 104.44 Å, c = 124.98 Å, α = β = 90°, γ = 120°. The collected X-ray diffraction data set is suitable for the solution of the three-dimensional structure of PRPPS at 3.1-Å resolution.

  16. 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.

  17. Crystallization and preliminary X-ray diffraction study of phosphoribosyl pyrophosphate synthetase from E. Coli

    Science.gov (United States)

    Timofeev, V. I.; Abramchik, Yu. A.; Zhukhlistova, N. E.; Kuranova, I. P.

    2015-09-01

    Enzymes of the phosphoribosyl pyrophosphate synthetase family (PRPPS, EC 2.7.6.1) catalyze the formation of 5-phosphoribosyl pyrophosphate (5-PRPP) from adenosine triphosphate and ribose 5-phosphate. 5-Phosphoribosyl pyrophosphate is an important intermediate in the synthesis of purine, pyrimidine, and pyridine nucleotides, as well as of the amino acids histidine and tryptophan. The crystallization conditions for E. coli PRPPS were found by the vapor-diffusion technique and were optimized to apply the capillary counter-diffusion technique. The X-ray diffraction data set was collected from the crystals grown by the counter-diffusion technique using a synchrotron radiation source to 3.1-Å resolution. The crystals of PRPPS belong to sp. gr. P6322 and have the following unit-cell parameters: a = b = 104.44 Å, c = 124.98 Å, α = β = 90°, γ = 120°. The collected X-ray diffraction data set is suitable for the solution of the three-dimensional structure of PRPPS at 3.1-Å resolution.

  18. 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.

  19. Hard X-ray diffraction enhanced imaging only using two crystals

    Institute of Scientific and Technical Information of China (English)

    LI Gang; WANG Nan; WU Ziyu

    2004-01-01

    Different configurations for the monochromator crystals and the analyzer crystals have been used in hard X-ray diffraction enhanced imaging (DEI) methods to overcome the complex task to adjust each of them to the ideal position. Here we present a very compact DEI configuration, and preliminary results of experiments performed at the Beijing Synchrotron Radiation Facility (BSRF) using only two crystals: the first one acting as monochromator and the second one as analyzer in the Bragg geometry. Refraction contrast images characterized by high contrast and spatial resolution are obtained and compared with absorption images. Differences among these images will be outlined and discussed emphasizing the potential capabilities of this very simple layout that guarantees a high transmission efficiency.

  20. 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.

  1. 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.

  2. 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.

  3. Redetermination of LaZn5 based on single crystal X-ray diffraction data

    Directory of Open Access Journals (Sweden)

    Igor Oshchapovsky

    2012-01-01

    Full Text Available The crystal structure of the already known binary title compound LaZn5 (lanthanum pentazinc (space group P6/mmm, Pearson symbol hP6, CaCu5 structure type has been redetermined from single-crystal X-ray diffraction data. In contrast to previous determinations based on X-ray powder data [Nowotny (1942. Z. Metallkd. 34, 247–253; de Negri et al. (2008. Intermetallics, 16, 168–178], where unit-cell parameters and assignment of the structure type were reported, the present study reveals anisotropic displacement parameters for all atoms. The crystal structure consists of three crytallographically distinct atoms. The La atom (Wyckoff site 1a, site symmetry 6/mmm is surrounded by 18 Zn atoms and two La atoms. The coordination polyhedron around one of the Zn atoms (Wyckoff site 2c, site symmetry -6m2 is an icosahedron made up from three La and nine Zn atoms. The other Zn atom (Wyckoff site 3g, site symmetry mmm is surrounded by four La and eight Zn atoms. Bonding between atoms is explored by means of the TB–LMTO–ASA (tight-binding linear muffin-tin orbital atomic spheres approximation program package. The positive charge density is localized around La atoms, and the negative charge density is around Zn atoms, with weak covalent bonding between the latter.

  4. 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.

  5. 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.

  6. Perfection of Apoferritin Crystals: An Advanced X-Ray Imaging and Diffraction Study

    Science.gov (United States)

    Hu, Z. W.; Thomas, B. R.; Chernov, A. A.; Chu, Y. S.

    2003-01-01

    Ferritin is a well-known iron-storage protein, and is a spherical shell that consists of 24 identical subunits packed in a 432 symmetry. The typically large protein size and its distinction from lysozyme as to chemical and physical characteristics make ferritin an attractive model protein for crystal growth and perfection investigation-as an alternative to the most widely studied lysozyme. In this contribution, the latest results obtained from coherence-based x-ray diffraction imaging and diffraction experiments will be presented on octahedral apoferritin (a demetalized form of ferritin) crystals grown from various growth conditions. Crystal specimens, which have the measured rocking-curve widths varying from a few arcseconds to several tens arcseconds (or more), are comparatively examined by intrinsically highly sensitive mapping of lattice perfection and defects. The richness of the observed defects and growth features offers insight into perfection and growth of protein crystals. Beautiful interference fringe patterns formed in diffraction images and fine oscillation structure of rocking curves observed will be discussed for understanding of physical origins and the underlying impact.

  7. In situ X-ray diffraction based investigation of crystallization in solution deposited PZT thin films

    Science.gov (United States)

    Nittala, Krishna

    Solution deposited PZT based thin films have potential applications in embedded decoupling capacitors and pulse discharge capacitors. During solution deposition, precursor solution is deposited onto a substrate to obtain an amorphous film. The film is then crystallized by heating it at a high temperature (˜600 - 700°C). Conditions during the crystallization anneal such as precursor stoichiometry in solution, heating rate and adhesion layer in the substrate are known to influence phase and texture evolution in these films. However, a mechanistic understanding of the changes taking place in these thin films during crystallization is lacking. A better understanding of the crystallization processes in these thin films could enable tailoring the properties of thin films to suit specific applications. To explore the crystallization process in solution deposited PZT thin films, high temperature in situ laboratory and synchrotron X-ray diffraction based techniques were developed. Taking advantage of the high X-ray flux available at synchrotron facilities such as beamline 6-ID-B, Advanced Photon Source, Argonne National Laboratory, crystalline phases formed in the thin films during crystallization at the high heating rates (0.5 -- 60°C/s) typically used during film processing could be measured. Using a 2-D detector for these measurements allowed the simultaneous measurement of both phase and texture information during crystallization. Analytical treatment of the unconventional diffraction geometry used during the synchrotron based measurements was performed to develop methodologies for quantitative estimation of texture components. The nominal lead content in the starting solutions and the heating rate used during crystallization was observed to influence the sequence of phases formed during crystallization of the films. In films crystallized at fast heating rates, titanium segregation, probably due to diffusion of titanium from the adhesion layer, was observed. To

  8. 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.

  9. Configuration Confirmation of Euphorbia Factor L1 by Single-crystal X-ray Diffraction

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    A 6,(17)-epoxylathyrol diterpenoid ((2S*3S*4R*5R*6S*9S*11S*15R*)-5,15-diacetoxy-3- phenylacetoxy-14-oxolathyra-6(17),(12E)-diene-6(17)-epoxide) was isolated from the seeds of Euhporbia lathyris L. Its configuration was puzzled because of the incomplete X-ray results reported before. In this work, the atom connectivity and configuration were confirmed by single-crystal X-ray diffraction together with ESI-MS, 1H-, and 13C-NMR spectroscopy. The compound crystallizes in monoclinic, space group P21 with a = 11.386(1), b = 8.2839(7), c = 17.192(2)(A), β = 108.305(2)o, Z = 2, V = 1539.5(2)(A)3, C32H40O8, Mr = 552.64, Dc = 1.192 g/m3, F(000) = 592, μ(MoKα) = 0.085 mm-1, T = 293(2) K, the final R = 0.0398 and wR = 0.0950 for 2057 observed reflections with I > 2σ(I). The molecule shows a tricyclic terpenoid skeleton, consisting of fused five-, eleven- and three-membered rings. The configuration at C(5) is R* and that at C(6) S*.

  10. X-ray diffraction: instrumentation and applications.

    Science.gov (United States)

    Bunaciu, Andrei A; Udriştioiu, Elena Gabriela; Aboul-Enein, Hassan Y

    2015-01-01

    X-ray diffraction (XRD) is a powerful nondestructive technique for characterizing crystalline materials. It provides information on structures, phases, preferred crystal orientations (texture), and other structural parameters, such as average grain size, crystallinity, strain, and crystal defects. X-ray diffraction peaks are produced by constructive interference of a monochromatic beam of X-rays scattered at specific angles from each set of lattice planes in a sample. The peak intensities are determined by the distribution of atoms within the lattice. Consequently, the X-ray diffraction pattern is the fingerprint of periodic atomic arrangements in a given material. This review summarizes the scientific trends associated with the rapid development of the technique of X-ray diffraction over the past five years pertaining to the fields of pharmaceuticals, forensic science, geological applications, microelectronics, and glass manufacturing, as well as in corrosion analysis.

  11. Third-order nonlinear and linear time-dependent dynamical diffraction of X-rays in crystals.

    Science.gov (United States)

    Balyan, Minas K

    2016-07-01

    For the first time the third-order nonlinear time-dependent Takagi's equations of X-rays in crystals are obtained and investigated. The third-order nonlinear and linear time-dependent dynamical diffraction of X-rays spatially restricted in the diffraction plane pulses in crystals is investigated theoretically. A method of solving the linear and the third-order nonlinear time-dependent Takagi's equations is proposed. Based on this method, results of analytical and numerical calculations for both linear and nonlinear diffraction cases are presented and compared.

  12. Expression, crystallization and preliminary X-ray diffraction studies of recombinant Clostridium perfringens β2-toxin

    Energy Technology Data Exchange (ETDEWEB)

    Gurjar, Abhijit A. [Department of Veterinary and Biomedical Science, The Pennsylvania State University (United States); Yennawar, Neela H.; Yennawar, Hemant P. [Macromolecular X-ray Crystallography Facility, The Pennsylvania State University (United States); Rajashankar, Kanagalaghatta R. [Argonne National Laboratory (United States); Hegde, Narasimha V.; Jayarao, Bhushan M., E-mail: bmj3@psu.edu [Department of Veterinary and Biomedical Science, The Pennsylvania State University (United States)

    2007-06-01

    The cloning, expression, purification and crystallization of recombinant Clostridium perfringens β2-toxin is described. The crystals diffracted to 2.9 Å resolution. Clostridium perfringens is a Gram-positive sporulating anaerobic bacterium that is responsible for a wide spectrum of diseases in animals, birds and humans. The virulence of C. perfringens is associated with the production of several enterotoxins and exotoxins. β2-toxin is a 28 kDa exotoxin produced by C. perfringens. It is implicated in necrotic enteritis in animals and humans, a disease characterized by a sudden acute onset with lethal hemorrhagic mucosal ulceration. The recombinant expression, purification and crystallization of β2-toxin using the batch-under-oil technique are reported here. Native X-ray diffraction data were obtained to 2.9 Å resolution on a synchrotron beamline at the F2 station at Cornell High Energy Synchrotron Source (CHESS) using an ADSC Quantum-210 CCD detector. The crystals belong to space group R3, with a dimer in the asymmetric unit; the unit-cell parameters are a = b = 103.71, c = 193.48 Å, α = β = 90, γ = 120° using the hexagonal axis setting. A self-rotation function shows that the two molecules are related by a noncrystallographic twofold axis with polar angles ω = 90.0, ϕ = 210.3°.

  13. 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.

  14. X-Ray Diffraction Apparatus

    Science.gov (United States)

    Blake, David F. (Inventor); Bryson, Charles (Inventor); Freund, Friedmann (Inventor)

    1996-01-01

    An x-ray diffraction apparatus for use in analyzing the x-ray diffraction pattern of a sample is introduced. The apparatus includes a beam source for generating a collimated x-ray beam having one or more discrete x-ray energies, a holder for holding the sample to be analyzed in the path of the beam, and a charge-coupled device having an array of pixels for detecting, in one or more selected photon energy ranges, x-ray diffraction photons produced by irradiating such a sample with said beam. The CCD is coupled to an output unit which receives input information relating to the energies of photons striking each pixel in the CCD, and constructs the diffraction pattern of photons within a selected energy range striking the CCD.

  15. Crystal structure of trirubidium citrate from laboratory X-ray powder diffraction data and DFT comparison.

    Science.gov (United States)

    Rammohan, Alagappa; Kaduk, James A

    2017-02-01

    The crystal structure of trirubidium citrate, 3Rb(+)·C6H5O7(3-), has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The two independent Rb(+) cations are seven- and eight-coordinate, with bond-valence sums of 0.99 and 0.92 valence units. The coordination polyhedra share edges and corners to form a three-dimensional framework. The only hydrogen bond is an intra-molecular one between the hy-droxy group and the central carboxyl-ate, with graph set S(5). The hydro-phobic methyl-ene groups lie in pockets in the framework.

  16. Crystal structure of trirubidium citrate from laboratory X-ray powder diffraction data and DFT comparison

    Science.gov (United States)

    Kaduk, James A.

    2017-01-01

    The crystal structure of trirubidium citrate, 3Rb+·C6H5O7 3−, has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The two independent Rb+ cations are seven- and eight-coordinate, with bond-valence sums of 0.99 and 0.92 valence units. The coordination polyhedra share edges and corners to form a three-dimensional framework. The only hydrogen bond is an intra­molecular one between the hy­droxy group and the central carboxyl­ate, with graph set S(5). The hydro­phobic methyl­ene groups lie in pockets in the framework. PMID:28217353

  17. Single crystal X-ray diffraction studies of DNA and DNA-drug complexes

    CERN Document Server

    Todd, A K

    1999-01-01

    The structure of the brominated oligonucleotide d(ACGTACG(5-BrU)) sub 2 was solved using the multiwavelength anomalous diffraction (MAD) technique. The space group was P4 sub 3 2 sub 1 2, with unit cell a=b=43.60A, c=26.27A. This structure was an A-DNA, isomorphous with many other previously solved octomers. Single crystal X-ray diffraction data were collected from crystals of the intercalation complexes N-[2-(dimethylamino)ethyl] acridine-4-carboxamide (DACA), d(CGTACG) sub 2 and N-[2-(dimethylamino)ethyl] 9-aminoacridine-4-carboxamide (9- aminoDACA) and some of their derivatives. An attempt was made to solve the structure of the DACA derivative N-[2-(dimethylamino)butyl]-acridine-4-carboxamide (DACA4) by molecular replacement, using the crystal structure of the daunomycin d(CGTACG) sub 2 complex as a search model. Attempts were made to position the molecule in the unit cell based on an SIR map, knowledge of the symmetry and unit cell dimensions. The structure of the 9-amino-5-bromo DACA - d(CGT(5-BrU)CG) su...

  18. Powder X-ray diffraction can differentiate between enantiomeric variants of calcium lactate pentahydrate crystal in cheese.

    Science.gov (United States)

    Tansman, G F; Kindstedt, P S; Hughes, J M

    2014-12-01

    Powder X-ray diffraction has been used for decades to identify crystals of calcium lactate pentahydrate in Cheddar cheese. According to this method, diffraction patterns are generated from a powdered sample of the crystals and compared with reference cards within a database that contains the diffraction patterns of known crystals. During a preliminary study of crystals harvested from various Cheddar cheese samples, we observed 2 slightly different but distinct diffraction patterns that suggested that calcium lactate pentahydrate may be present in 2 different crystalline forms. We hypothesized that the 2 diffraction patterns corresponded to 2 enantiomeric forms of calcium lactate pentahydrate (L- and DL-) that are believed to occur in Cheddar cheese, based on previous studies involving enzymatic analyses of the lactate enantiomers in crystals obtained from Cheddar cheeses. However, the powder X-ray diffraction database currently contains only one reference diffraction card under the title “calcium lactate pentahydrate.” To resolve this apparent gap in the powder X-ray diffraction database, we generated diffraction patterns from reagent-grade calcium l-lactate pentahydrate and laboratory-synthesized calcium dl-lactate pentahydrate. From the resulting diffraction patterns we determined that the existing reference diffraction card corresponds to calcium dl-lactate pentahydrate and that the other form of calcium lactate pentahydrate observed in cheese crystals corresponds to calcium l-lactate pentahydrate. Therefore, this report presents detailed data from the 2 diffraction patterns, which may be used to prepare 2 reference diffraction cards that differentiate calcium l-lactate pentahydrate from calcium dl-lactate pentahydrate. Furthermore, we collected crystals from the exteriors and interiors of Cheddar cheeses to demonstrate the ability of powder X-ray diffraction to differentiate between the 2 forms of calcium lactate pentahydrate crystals in Cheddar cheeses

  19. 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...

  20. Statistical dynamical theory of X-ray diffraction in the Bragg case: application to triple-crystal diffractometry

    Science.gov (United States)

    Pavlov; Punegov

    2000-05-01

    The statistical dynamical theory of X-ray diffraction is developed for a crystal containing statistically distributed microdefects. Fourier-component equations for coherent and diffuse (incoherent) scattered waves have been obtained in the case of so-called triple-crystal diffractometry. New correlation lengths and areas are introduced for characterization of the scattered volume.

  1. 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.

  2. The Dynamical Theory of X Ray Diffraction

    Science.gov (United States)

    Balchin, A. A.; Whitehouse, C. R.

    1974-01-01

    Summarizes the Darwin theory of x-ray diffraction in thin crystals or crystals with a mosaic texture and its modified application to crystals with three-dimensional electrostatic dipoles. Indicates that the dynamical theory is brought into its present relevance by the improvement of single crystal growth techniques. (CC)

  3. 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.

  4. Crystal structure of nitarsone determined from synchrotron X-ray powder diffraction data

    Science.gov (United States)

    van der Lee, A.; Richez, P.; Tapiero, C.

    2005-05-01

    The crystal structure of nitarsone, 4-nitrophenylarsonic acid, a substitute for nifursol and dimetridazole in the prevention and treatment of turkey histomoniasis desease, has been determined from synchrotron X-ray powder diffraction data. Nitarsone crystallizes in the monoclinic space group P2 1/ n with unit cell parameters a=7.46413(5), b=25.68543(17), c=4.657388(32) Å, β=105.4670(5)°. The structure was solved using simulated annealing techniques by treating the molecule as a rigid body for which the configuration resulting from an energy minimization was used in slightly adapted form. Structure refinement treated the NO 2 and the AsO(OH) 2 groups as free groups, leading to final confidence factors Rp=0.059 and Rwp=0.071. The crystal structure contains 4 molecules per unit cell that are hydrogen bonded to form infinite chains of dimers running along the c-axis. Nitarsone's low toxicity when compared with inorganic sources of arsenic is explained by the existence of a partial double C-As bond (1.866(5) Å) which confers greater stability so that under physiological conditions nitarsone is not converted to mineral-like As V or III.

  5. Single-Crystal X-Ray Diffraction of Pyrope Garnet to 84 GPa

    Science.gov (United States)

    Finkelstein, G. J.; Dera, P. K.; Duffy, T. S.

    2012-12-01

    Garnets are characteristic minerals of many metamorphic and igneous rocks, and are also important upper-mantle constituents. Mg-rich (pyrope) garnets occur in both peridotite and eclogite compositions in the upper mantle. At high temperatures and pressures above 25 GPa, garnets transform to the perovskite structure. The post-garnet transition kinetics are sluggish, and in cold subducting slabs garnets could persist metastably at temperatures as high as 1700 K on geological timescales. These phases could add positive buoyancy to a subducting slab, inhibiting subduction. There has been minimal previous work on the 300 K compression behavior of aluminosilicate garnets at pressures higher than 10 GPa. In this work, we have collected single-crystal X-ray diffraction data on near end-member natural pyrope (Dora Maira pyrope) to 84 GPa. By extending the compression of pyrope to much higher pressures, we can better constrain the equation of state while also characterizing the structural response to such extreme pressures for the first time. Crystals were polished to ~5-10 μm in thickness, and loaded in a diamond anvil cell with gold foil and ruby balls as pressure calibrants. Helium was used as a pressure-transmitting medium. High-pressure single-crystal X-ray diffraction experiments were performed at the GSECARS 13-ID-D beamline of the Advanced Photon Source and the 12.2.2 beamline of the Advanced Light Source. Structure refinements were carried out successfully to the highest pressure using Shelx-97, extending the range over which the compression behavior of this material has been characterized by a factor of nearly three. Pyrope exhibits smooth compression behavior and no phase transitions over the investigated pressure range. A preliminary 3rd order Birch-Murnaghan equation of state was successfully fit to data up to 52 GPa. If the bulk modulus is fixed to 170 GPa, a value consistent with previous Brillouin and Ultrasonic studies, our data yields a pressure derivative

  6. Computer simulations of X-ray six-beam diffraction in a perfect silicon crystal. I.

    Science.gov (United States)

    Kohn, V G; Khikhlukha, D R

    2016-05-01

    This paper reports computer simulations of the transmitted-beam intensity distribution for the case of six-beam (000, 220, 242, 044, -224, -202) diffraction of X-rays in a perfect silicon crystal of thickness 1 mm. Both the plane-wave angular dependence and the six-beam section topographs, which are usually obtained in experiments with a restricted beam (two-dimensional slit), are calculated. The angular dependence is calculated in accordance with Ewald's theory. The section topographs are calculated from the angular dependence by means of the fast Fourier transformation procedure. This approach allows one to consider, for the first time, the transformation of the topograph's structure due to the two-dimensional slit sizes and the distance between the slit and the detector. The results are in good agreement with the results of other works and with the experimental data. This method of calculation does not require a supercomputer and it was performed on a standard laptop. A detailed explanation of the main features of the diffraction patterns at different distances between the slit and the detector is presented.

  7. X-ray-excited optical luminescence of protein crystals: a new tool for studying radiation damage during diffraction data collection.

    Science.gov (United States)

    Owen, Robin L; Yorke, Briony A; Pearson, Arwen R

    2012-05-01

    During X-ray irradiation protein crystals radiate energy in the form of small amounts of visible light. This is known as X-ray-excited optical luminescence (XEOL). The XEOL of several proteins and their constituent amino acids has been characterized using the microspectrophotometers at the Swiss Light Source and Diamond Light Source. XEOL arises primarily from aromatic amino acids, but the effects of local environment and quenching within a crystal mean that the XEOL spectrum of a crystal is not the simple sum of the spectra of its constituent parts. Upon repeated exposure to X-rays XEOL spectra decay non-uniformly, suggesting that XEOL is sensitive to site-specific radiation damage. However, rates of XEOL decay were found not to correlate to decays in diffracting power, making XEOL of limited use as a metric for radiation damage to protein crystals. © 2012 International Union of Crystallography

  8. 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.

  9. Crystallization of medium length 1-alcohols in mesoporous silicon: An X-ray diffraction study

    CERN Document Server

    Henschel, Anke; Knorr, Klaus

    2008-01-01

    The linear 1-alcohols n-C16H33OH, n-C17H35OH, n-C19H37OH have been imbibed and solidified in lined up, tubular mesopores of silicon with 10 nm and 15 nm mean diameters, respectively. X-ray diffraction measurements reveal a set of six discrete orientation states (''domains'') characterized by a perpendicular alignment of the molecules with respect to the long axis of the pores and by a four-fold symmetry about this direction, which coincides with the crystalline symmetry of the Si host. A Bragg peak series characteristic of the formation of bilayers indicates a lamellar structure of the spatially confined alcohol crystals in 15 nm pores. By contrast, no layering reflections could be detected for 10 nm pores. The growth mechanism responsible for the peculiar orientation states is attributed to a nano-scale version of the Bridgman technique of single-crystal growth, where the dominant growth direction is aligned parallelly to the long pore axes. Our observations are analogous to the growth phenomenology encounte...

  10. Studies on Crystal Orientation of ZnO Film on Sapphire Using High-throughout X-ray Diffraction

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The orientation of the nano-columnar ZnO films grown on sapphire using the technique of metal-organic chemical vapor deposition (MOCVD) exhibits deviation because of the mismatch between the crystal lattices of the films and the sapphire substrate. A high-throughout X-ray diffraction method was employed to determine the crystal orientation of the ZnO films at a time scale of the order of minutes based on the general area detection diffraction system (GADDS). This rapid, effective, and ready method, adapted for characterizing the orientation of the nano-columnar crystals is used to directly explain the results of observation of the X-ray diffraction images, by the measurements of the orientations of the crystal columns of the ZnO films along c-axis and in parallel to ab plane.

  11. Crystal Structure and X-ray Powder Diffraction Data for Rare Earth Compound PrNiSn

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    The compound PrNiSn was studied by X-ray powder diffraction technique. The crystal structure and the X-ray diffraction data for this compound at room temperature were reported. The compound PrNiSn is orthorhombic with lattice parameters a=0.74569(3) nm, b=0.76851(5) nm, c=0.45676(8) nm, V=0.26176 nm3, Z=4 and Dx=8.076 g·cm-3, space group Pna21(33). The figure of merit FN for the compound is F30=54 (0.0093, 60).

  12. Time-dependent Takagi-Taupin eikonal theory of X-ray diffraction in rapidly changing crystal structures.

    Science.gov (United States)

    Adams, Bernhard W

    2004-03-01

    The Takagi-Taupin theory is extended by synthesizing it with the eikonal theory in a unified space-time approach based upon microscopic electromagnetism. The principal goal is the description of X-ray diffraction in a crystal undergoing subpicosecond and few-femtosecond changes.

  13. SCALING OF X-RAY-DIFFRACTION INTENSITIES FOR CRYSTALS WITH A ONE-DIMENSIONAL, INCOMMENSURATE, DISPLACIVE MODULATION

    NARCIS (Netherlands)

    LAM, EJW; BEURSKENS, PT; VANSMAALEN, S

    1992-01-01

    A statistical method is presented for the determination of the scale factor, an overall isotropic temperature factor and an overall modulation amplitude from the X-ray diffraction intensities of crystals with a one-dimensional, incommensurate, displacive modulation. Application to several compounds

  14. High-pressure X-ray diffraction of L-ALANINE crystal

    DEFF Research Database (Denmark)

    Olsen, J.S.; Gerward, Leif; Souza, A.G.

    2006-01-01

    L-ALANINE has been studied by X-ray diffraction at ambient temperature and pressure up to 10.3 GPa. The material is found to transform to a tetragonal structure between 2 and 3 GPa. and to a monoclinic structure between 8 and 10 GPa. The experimental bulk modulus is 25(5) GPa for the orthorhombic...

  15. High-pressure X-ray diffraction of L-ALANINE crystal

    DEFF Research Database (Denmark)

    Olsen, J.S.; Gerward, Leif; Souza, A.G.

    2006-01-01

    L-ALANINE has been studied by X-ray diffraction at ambient temperature and pressure up to 10.3 GPa. The material is found to transform to a tetragonal structure between 2 and 3 GPa. and to a monoclinic structure between 8 and 10 GPa. The experimental bulk modulus is 25(5) GPa for the orthorhombic...

  16. Crystallization and preliminary X-ray diffraction of the Munc18c–syntaxin4{sub 1–29} complex

    Energy Technology Data Exchange (ETDEWEB)

    Latham, Catherine F.; Hu, Shu-Hong; Gee, Christine L.; Armishaw, Chris J.; Alewood, Paul F. [Institute for Molecular Bioscience and Special Research Centre for Functional and Applied Genomics, The University of Queensland, Brisbane, QLD 4072 (Australia); James, David E. [Garvan Institute of Medical Research, Darlinghurst, NSW 2010 (Australia); Martin, Jennifer L., E-mail: j.martin@imb.uq.edu.au [Institute for Molecular Bioscience and Special Research Centre for Functional and Applied Genomics, The University of Queensland, Brisbane, QLD 4072 (Australia)

    2007-06-01

    Cocrystallization with a peptide, free-interface diffusion crystal chips and crystal dehydration were important in the production of diffraction-quality crystals of the Munc18c protein that helps to regulate membrane fusion. The production of diffraction-quality crystals of Munc18c, a protein involved in regulating vesicular exocytosis in mammals, is reported. The diffraction resolution of Munc18c crystals was optimized by (i) cocrystallizing with a peptide fragment of the Munc18c functional binding partner syntaxin4, (ii) using nanolitre free-interface diffusion crystallization-screening chips and microlitre hanging-drop vapour diffusion and (iii) applying a post-crystallization dehydration treatment. Crystals belonging to the cubic space group P2{sub 1}3, with unit-cell parameters a = b = c = 170.8 Å, α = β = γ = 90°, were generated that diffract to 3.7 Å resolution on a laboratory X-ray source.

  17. 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.

  18. 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.

  19. Investigation on quality of cubic GaN/GaAs (100) by double-crystal X-ray diffraction

    Institute of Scientific and Technical Information of China (English)

    徐大鹏; 王玉田; 杨辉; 郑联喜; 李建斌; 段俐宏; 吴荣汉

    1999-01-01

    Cubic GaN was grown on GaAs (100) by low pressure metal organic chemical vapor deposition (MOCVD). X-ray diffraction, scanning electron microscope (SEM) and photoluminescence (PL) spectra were performed to characterize the quality of the GaN film. The PL spectra of cubic GaN thin films being thicker than 1.5 μm were reported. Triple-crystal diffraction to analyze orientation distributions and strain of the thin films was also demonstrated.

  20. Crystallization and preliminary X-ray diffraction study of recombinant ribokinase from Thermus Species 2.9

    Science.gov (United States)

    Abramchik, Yu. A.; Timofeev, V. I.; Muravieva, T. I.; Esipov, R. S.; Kuranova, I. P.

    2016-11-01

    Ribokinase from a thermophilic strain of Thermus species 2.9 belonging to the carbohydrate ribokinase family (EC 2.7.1.15) was isolated, purified, and crystallized. The crystallization conditions were found by the vapor-diffusion technique and were then optimized to apply the capillary counter-diffusion technique. The X-ray diffraction data set was collected from the crystals, which were grown by the counter-diffusion technique, at the SPring-8 synchrotron radiation facility to 2.87 Å resolution. The crystals belong to sp. gr. P1211 and have the following unit-cell parameters: a = 81.613 Å, b = 156.132 Å, c = 87.714 Å, α = γ = 90°, β = 103.819°. The X-ray diffraction data set is suitable for determining the three-dimensional structure of the protein by the molecular-replacement method.

  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 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.

  3. Isolation, purification, crystallization, and preliminary X-ray diffraction study of the crystals of HU protein from M. gallisepticum

    Science.gov (United States)

    Nikolaeva, A. Yu.; Timofeev, V. I.; Boiko, K. M.; Korzhenevskii, D. A.; Rakitina, T. V.; Dorovatovskii, P. V.; Lipkin, A. V.

    2015-11-01

    HU proteins are involved in bacterial DNA and RNA repair. Since these proteins are absent in cells of higher organisms, inhibitors of HU proteins can be used as effective and safe antibiotics. The crystallization conditions for the M. gallisepticum HU protein were found and optimized by the vapor-diffusion method. The X-ray diffraction data set was collected to 2.91 Å resolution from the crystals grown by the vapor-diffusion method on a synchrotron source. The crystals of the HU protein belong to sp. gr. P41212 and have the following unit-cell parameters: a = b = 97.94 Å, c = 77.92 Å, α = β = γ = 90°.

  4. Crystallization and preliminary X-ray diffraction study of phosphopantetheine adenylyltransferase from M. tuberculosis crystallizing in space group P32

    Science.gov (United States)

    Timofeev, V. I.; Chupova, L. A.; Esipov, R. S.; Kuranova, I. P.

    2015-09-01

    Crystals of M. tuberculosis phosphopantetheine adenylyltransferase 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 2.00-Å resolution. The crystals belong to sp. gr. P32 and have the following unit-cell parameters: a = b = 106.47 Å, c = 71.32 Å, α = γ = 90°, β = 120°. The structure was solved by the molecular-replacement method. There are six subunits of the enzyme comprising a hexamer per asymmetric unit. The hexamer is a biologically active form of phosphopantetheine adenylyltransferase from M. tuberculosis.

  5. X-ray Multiple Diffraction Topographic Imaging Technique For Growth History Study of Habit Modifying Impurity Doped Crystals

    Institute of Scientific and Technical Information of China (English)

    LAI X.; MA C.; K. J. Robert; M. C. Miller

    2004-01-01

    A novel crystal characterization instrument has been built up in which a combination of X-ray multiple diffraction and X-ray topography is applied to enabling the cross-correlation between micro-crystallographic symmetry and its spatial dependence in relation to lattice defects. This facility is used to examine, in a selfconsistent manner, growth sector-dependant changes to both the crystallographic structure and the lattice defects associated with the action of habit-modifying additives in a number of representative crystal growth systems. In addition, the new instrument can be used to probe micro-crystallographic aspects (such as distortion to crystal symmetry) and relate these in a spatially resolved manner to the crystal defect structure in crystals doped with known habit modifiers.

  6. Recombinant formate dehydrogenase from Arabidopsis thaliana: Preparation, crystal growth in microgravity, and preliminary X-ray diffraction study

    Energy Technology Data Exchange (ETDEWEB)

    Shabalin, I. G., E-mail: inna@ns.crys.ras.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation); Serov, A. E.; Skirgello, O. E. [Moscow State University, Faculty of Chemistry (Russian Federation); Timofeev, V. I.; Samygina, V. R. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation); Popov, V. O. [Russian Academy of Sciences, Bach Institute of Biochemistry (Russian Federation); Tishkov, V. I. [Moscow State University, Faculty of Chemistry (Russian Federation); Kuranova, I. P. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2010-09-15

    Crystals of high-purity recombinant NAD{sup +}-dependent formate dehydrogenase from the higher plant Arabidopsis thaliana (AraFDH) were grown in microgravity in the Modul'-1 protein crystallization apparatus on the International Space Station. The space-grown crystals have larger sizes than those grown on Earth. X-ray diffraction data suitable for determining the three-dimensional structure were collected from the space-grown crystals to a resolution of 1.22 A using an X-ray synchrotron source. The crystals belong to sp. gr. P4{sub 3}2{sub 1}2; the unit-cell parameters are a = b = 107.865 A, c = 71.180 A, {alpha} = {beta} = {gamma} = 90 deg.

  7. Crystal Tilts in Epitaxially Laterally Overgrown GaN Films Determined by Four-Circle X-Ray Diffraction

    Institute of Scientific and Technical Information of China (English)

    汪峰; 张荣; 陈志忠; 吴小山; 顾书林; 沈波; 郑有堃; 蒋树声

    2001-01-01

    Crystal tilts in epitaxially laterally overgrown (ELO) GaN films via hydride vapour phase epitaxy (HVPE) onsapphire substrates have been investigated by using the four-circle x-ray diffraction method. Three diffractionpeaks corresponding to the (0002) reflection of vertically epitaxial and tilted GaN domains are observable in thex-ray rocking curve. The angle separations △ω between the main peak and two lobes change with the azimuthangle φ. The dependence of △ω on φ and the crystal tilt angle θ has been calculated based on the standardkinetic x-ray diffraction model. The crystal tilt angle of a typical HVPE ELO GaN sample has been determinedto be 2.379°.

  8. 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.

  9. Redetermination of the crystal structure of β-zinc molybdate from single-crystal X-ray diffraction data.

    Science.gov (United States)

    Mtioui-Sghaier, Olfa; Mendoza-Meroño, Rafael; Ktari, Lilia; Dammak, Mohamed; García-Granda, Santiago

    2015-07-01

    The crystal structure of the β-polymorph of ZnMoO4 was re-determined on the basis of single-crystal X-ray diffraction data. In comparison with previous powder X-ray diffraction studies [Katikaneani & Arunachalam (2005 ▸). Eur. J. Inorg. Chem. pp. 3080-3087; Cavalcante et al. (2013 ▸). Polyhedron, 54, 13-25], all atoms were refined with anisotropic displacement parameters, leading to a higher precision with respect to bond lengths and angles. β-ZnMoO4 adopts the wolframite structure type and is composed of distorted ZnO6 and MoO6 octa-hedra, both with point group symmetry 2. The distortion of the octa-hedra is reflected by variation of bond lengths and angles from 2.002 (3)-2.274 (4) Å, 80.63 (11)-108.8 (2)° for equatorial and 158.4 (2)- 162.81 (14)° for axial angles (ZnO6), and of 1.769 (3)-2.171 (3) Å, 73.39 (16)-104.7 (2), 150.8 (2)-164.89 (15)° (MoO6), respectively. In the crystal structure, the same type of MO6 octa-hedra share edges to built up zigzag chains extending parallel to [001]. The two types of chains are condensed by common vertices into a framework structure. The crystal structure can alternatively be described as derived from a distorted hexa-gonally closed packed arrangement of the O atoms, with Zn and Mo in half of the octa-hedral voids.

  10. Redetermination of the crystal structure of β-zinc molybdate from single-crystal X-ray diffraction data

    Directory of Open Access Journals (Sweden)

    Olfa Mtioui-Sghaier

    2015-07-01

    Full Text Available The crystal structure of the β-polymorph of ZnMoO4 was re-determined on the basis of single-crystal X-ray diffraction data. In comparison with previous powder X-ray diffraction studies [Katikaneani & Arunachalam (2005. Eur. J. Inorg. Chem. pp. 3080–3087; Cavalcante et al. (2013. Polyhedron, 54, 13–25], all atoms were refined with anisotropic displacement parameters, leading to a higher precision with respect to bond lengths and angles. β-ZnMoO4 adopts the wolframite structure type and is composed of distorted ZnO6 and MoO6 octahedra, both with point group symmetry 2. The distortion of the octahedra is reflected by variation of bond lengths and angles from 2.002 (3–2.274 (4 Å, 80.63 (11–108.8 (2° for equatorial and 158.4 (2– 162.81 (14° for axial angles (ZnO6, and of 1.769 (3–2.171 (3 Å, 73.39 (16–104.7 (2, 150.8 (2–164.89 (15° (MoO6, respectively. In the crystal structure, the same type of MO6 octahedra share edges to built up zigzag chains extending parallel to [001]. The two types of chains are condensed by common vertices into a framework structure. The crystal structure can alternatively be described as derived from a distorted hexagonally closed packed arrangement of the O atoms, with Zn and Mo in half of the octahedral voids.

  11. Performance characteristics needed for protein crystal diffraction x-ray detectors.

    Energy Technology Data Exchange (ETDEWEB)

    Westbrook, E. M.

    1999-09-21

    During the 1990's, macromolecular crystallography became progressively more dependent on synchrotrons X-ray sources for diffraction data collection. Detectors of this diffraction data at synchrotrons beamlines have evolved over the decade, from film to image phosphor plates, and then to CCD systems. These changes have been driven by the data quality and quantity improvements each newer detector technology provided. The improvements have been significant. It is likely that newer detector technologies will be adopted at synchrotron beamlines for crystallographic diffraction data collection in the future, but these technologies will have to compete with existing CCD detector systems which are already excellent and are getting incrementally better in terms of size, speed, efficiency, and resolving power. Detector development for this application at synchrotrons must concentrate on making systems which are bigger and faster than CCDs and which can capture weak data more efficiently. And there is a need for excellent detectors which are less expensive than CCD systems.

  12. 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.

  13. Note: application of a pixel-array area detector to simultaneous single crystal X-ray diffraction and X-ray absorption spectroscopy measurements.

    Science.gov (United States)

    Sun, Cheng-Jun; Zhang, Bangmin; Brewe, Dale L; Chen, Jing-Sheng; Chow, G M; Venkatesan, T; Heald, Steve M

    2014-04-01

    X-ray diffraction (XRD) and X-ray absorption spectroscopy (XAS) are two main x-ray techniques in synchrotron radiation facilities. In this Note, we present an experimental setup capable of performing simultaneous XRD and XAS measurements by the application of a pixel-array area detector. For XRD, the momentum transfer in specular diffraction was measured by scanning the X-ray energy with fixed incoming and outgoing x-ray angles. By selecting a small fixed region of the detector to collect the XRD signal, the rest of the area was available for collecting the x-ray fluorescence for XAS measurements. The simultaneous measurement of XRD and X-ray absorption near edge structure for Pr0.67Sr0.33MnO3 film was demonstrated as a proof of principle for future time-resolved pump-probe measurements. A static sample makes it easy to maintain an accurate overlap of the X-ray spot and laser pump beam.

  14. 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.

  15. 7 Å resolution in protein two-dimensional-crystal X-ray diffraction at Linac Coherent Light Source.

    Science.gov (United States)

    Pedrini, Bill; Tsai, Ching-Ju; Capitani, Guido; Padeste, Celestino; Hunter, Mark S; Zatsepin, Nadia A; Barty, Anton; Benner, W Henry; Boutet, Sébastien; Feld, Geoffrey K; Hau-Riege, Stefan P; Kirian, Richard A; Kupitz, Christopher; Messerschmitt, Marc; Ogren, John I; Pardini, Tommaso; Segelke, Brent; Williams, Garth J; Spence, John C H; Abela, Rafael; Coleman, Matthew; Evans, James E; Schertler, Gebhard F X; Frank, Matthias; Li, Xiao-Dan

    2014-07-17

    Membrane proteins arranged as two-dimensional crystals in the lipid environment provide close-to-physiological structural information, which is essential for understanding the molecular mechanisms of protein function. Previously, X-ray diffraction from individual two-dimensional crystals did not represent a suitable investigational tool because of radiation damage. The recent availability of ultrashort pulses from X-ray free-electron lasers (XFELs) has now provided a means to outrun the damage. Here, we report on measurements performed at the Linac Coherent Light Source XFEL on bacteriorhodopsin two-dimensional crystals mounted on a solid support and kept at room temperature. By merging data from about a dozen single crystal diffraction images, we unambiguously identified the diffraction peaks to a resolution of 7 Å, thus improving the observable resolution with respect to that achievable from a single pattern alone. This indicates that a larger dataset will allow for reliable quantification of peak intensities, and in turn a corresponding increase in the resolution. The presented results pave the way for further XFEL studies on two-dimensional crystals, which may include pump-probe experiments at subpicosecond time resolution. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  16. Neutron and X-ray single-crystal diffraction from protein microcrystals via magnetically oriented microcrystal arrays in gels.

    Science.gov (United States)

    Tsukui, Shu; Kimura, Fumiko; Kusaka, Katsuhiro; Baba, Seiki; Mizuno, Nobuhiro; Kimura, Tsunehisa

    2016-07-01

    Protein microcrystals magnetically aligned in D2O hydrogels were subjected to neutron diffraction measurements, and reflections were observed for the first time to a resolution of 3.4 Å from lysozyme microcrystals (∼10 × 10 × 50 µm). This result demonstrated the possibility that magnetically oriented microcrystals consolidated in D2O gels may provide a promising means to obtain single-crystal neutron diffraction from proteins that do not crystallize at the sizes required for neutron diffraction structure determination. In addition, lysozyme microcrystals aligned in H2O hydrogels allowed structure determination at a resolution of 1.76 Å at room temperature by X-ray diffraction. The use of gels has advantages since the microcrystals are measured under hydrated conditions.

  17. Structural characterization of three crystalline modifications of telmisartan by single crystal and high-resolution X-ray powder diffraction.

    Science.gov (United States)

    Dinnebier, R E; Sieger, P; Nar, H; Shankland, K; David, W I

    2000-11-01

    Three crystalline modifications (A, B, and C) of 4'-[[2-n-propyl-4-methyl-6-(1-methyl-benzimidazol-2-yl)benzi midazol-1-yl]methyl]biphenyl-2-carboxylic acid (INN name, telmisartan) have been detected and their crystal structures have been determined by single-crystal X-ray diffraction (pseudopolymorph C) and the method of simulated annealing from high-resolution X-ray powder diffraction data (polymorphs A and B). The compound is of interest because of its use as an angiotensin II receptor antagonist. Polymorph A crystallizes in space group P2(I)/c, Z = 4, with unit cell parameters a = 18.7798(3), b = 18.1043(2), and c = 8.00578(7) A, beta = 97.066(1) degrees, and V = 2701.31 A(3). Polymorph B crystallizes in space group P2(I)/a, Z = 4, with unit cell parameters a = 16.0646(5), b = 13.0909(3), and c = 13.3231(3) A, beta = 99.402(1) degrees, and V = 2764.2(1) A(3). The solvated form C crystallizes in space group C2/c, Z = 8, with unit cell parameters a = 30.990(5), b = 13.130(3), and c = 16.381(3) A, beta = 95.02(2) degrees, and V = 6639(2) A(3). For the structure solutions of polymorphs A and B, 13 degrees of freedom (3 translational, 3 orientational, 7 torsion angles) were determined in approximately 2 h of computer time, demonstrating that the crystal packing and the molecular conformation of medium-sized (MW approximately 500) pharmaceutical compounds can now be solved quickly and routinely from high-resolution X-ray powder diffraction data.

  18. [X-ray diffraction spectrum of heroin].

    Science.gov (United States)

    Hu, X; Kan, J; Yuan, B

    1999-06-01

    In this paper, practical measured X-ray diffraction spectra of heroin and opium are given and the parameters of each diffraction peak of the heroin are listed. The heroin belongs to orthorhombic crystal system; the basic vectors of the primitive cell are: a = 8.003, b = 14.373, c = 16.092 x 10(-10) m. As compared with the standard spectra of pure heroin and sucrose, the main doped additive checked by us, is sugar affirmatively.

  19. Crystal structure and tautomerism of Pigment Yellow 138 determined by X-ray powder diffraction and solid-state NMR

    DEFF Research Database (Denmark)

    Gumbert, Silke D.; Körbitzer, Meike; Alig, Edith;

    2016-01-01

    The crystal structure of C.I. Pigment Yellow 138 was determined from X-ray powder diffraction data using real-space methods with subsequent Rietveld refinements. The tautomeric state was investigated by solid-state 1D and 2D multinuclear NMR experiments. In the crystals, the compound exhibits...... the NH-tautomer with a hydrogen atom situated at the nitrogen of the quinoline moiety. Direct evidence of the presence of the NH-tautomer is provided by 1H–14N HMQC solid-state NMR at very fast MAS. Solid-state dispersion-corrected density functional theory calculations with BLYP-D3 confirm...

  20. 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.

  1. Purification, crystallization and preliminary X-ray diffraction studies of C-phycocyanin and allophycocyanin from Spirulina platensis.

    Science.gov (United States)

    Moreno, A; Bermejo, R; Talavera, E; Alvarez-Pez, J M; Sanz-Aparicio, J; Romero-Garrido, A

    1997-05-01

    C-phycocyanin and allophycocyanin from the green alga Spirulina platensis were isolated and crystallized by gel-acupuncture techniques. A novel two-step chromatographic procedure was used for purification. Blue hexagonal crystals were obtained by diffusing magnesium chloride into the protein solution for a week, followed by diffusion of PEG 6000 in order to complete the reduction of the solubility of the protein in the capillary tube used as a growth cell. In the case of allophycocyanin, crystals with a size of 0.4 x 0.3 x 0.3 mm were characterized by X-ray diffraction. They belong to space group P6(3)22 with unit-cell parameters a = b = 102.04, c = 131.22 A. The crystals of C-phycocyanin belong to either space group P6 or P6(3) with unit-cell constants a = b = 182.38, c = 60.87 A, alpha = beta = 90, gamma = 120 degrees. The crystals diffract beyond 2.4 and 2.5 A resolution, respectively, using a rotating anode as an X-ray source.

  2. 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.

  3. 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.

  4. X-ray Excited Optical Fluorescence and Diffraction Imaging of Reactivity and Crystallinity in a Zeolite Crystal : Crystallography and Molecular Spectroscopy in One

    NARCIS (Netherlands)

    Ristanovic, Zoran; Hofmann, Jan P; Richard, Marie-Ingrid; Jiang, Tao; Chahine, Gilbert A; Schülli, Tobias U; Meirer, Florian; Weckhuysen, Bert M

    2016-01-01

    Structure-activity relationships in heterogeneous catalysis are challenging to be measured on a single-particle level. For the first time, one X-ray beam is used to determine the crystallographic structure and reactivity of a single zeolite crystal. The method generates μm-resolved X-ray diffraction

  5. On the Use of Wide-Angle Energy-Sensitive Detectors in White-Beam X-Ray Single-Crystal Diffraction

    DEFF Research Database (Denmark)

    Buras, B.; Staun Olsen, J.; Gerward, Leif

    1980-01-01

    The possible applications of multiple-element or large-area semiconductor detectors in single-crystal X-ray diffraction are discussed on the basis of experimental results using Bremsstrahlung as well as synchrotron radiation.......The possible applications of multiple-element or large-area semiconductor detectors in single-crystal X-ray diffraction are discussed on the basis of experimental results using Bremsstrahlung as well as synchrotron radiation....

  6. 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}.

  7. [Study on the hydrolysis distribution of ferric saline by infrared spectrophotometry and single crystal X-ray diffraction method].

    Science.gov (United States)

    Zheng, Huai-Li; Xie, Li-Guo; Gao, Chao-Yong; Sun, Xiu-Ping; Yang, You; Tang, Xue

    2009-02-01

    The hydrolytic stability of Fe(a), Fe(b) and Fe(c) in different pH values of poly-ferric-flocculants was studied by using Fe-ferron time by time complexation colorimetry. The research results showed that Fe(b) was unstable, and all Fe(b) was transformed to Fe(c) after 10-15 d placement. The content of Fe(c) tended towards stability after 10-15 d. Also, the content of Fe(a) tended towards stability after 10 d. The single crystal was synthesized by the method of direct crystallization in Fe(III)-SO4(2-) water solution at normal temperature and its structure characteristic was studied by single crystal X ray diffraction method and IR (infrared spectrophotometry). The research results showed that there was no group of Fe-OH-Fe, Fe-OH and binary ferric complexed with two hydroxyl groups in the single crystal synthesized from the ferric aqueous solution in low pH (pH was about 0.5). The form of Fe in single crystal was all Fe(III). The chemical formula of the single crystal was Fe(H2O)6 (SO4)2NH4 x 6H2O when the ammonia water was used as the alkalinizing agent. One reason was that with the evaporation of water, these single crystals were synthesized at pH 0. 5 despite of different initial pH and different initial alkalinizing agents. Another reason was that the hydrolysis distribution of ferric saline was unstable. Therefore, it was not easy to obtain the single crystal of Fe(III)-hydroxy complexes or Fe(III)-polymer at low pH value. The study showed that infrared spectrophotometry and single crystal X ray diffraction method have a good prospect in the research on hydrolysis distribution of flocculants.

  8. Crystal structure of caesium dihydrogen citrate from laboratory X-ray powder diffraction data and DFT comparison

    Directory of Open Access Journals (Sweden)

    Alagappa Rammohan

    2017-02-01

    Full Text Available The crystal structure of caesium dihydrogen citrate, Cs+·H2C6H5O7−, has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The coordination polyhedra of the nine-coordinate Cs+ cations share edges to form chains along the a-axis. These chains are linked by corners along the c-axis. The un-ionized carboxylic acid groups form two different types of hydrogen bonds; one forms a helical chain along the c-axis, and the other is discrete. The hydroxy group participates in both intra- and intermolecular hydrogen bonds.

  9. 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.

  10. Crystallization and preliminary X-ray diffraction studies of Murraya koenigii trypsin inhibitor

    Science.gov (United States)

    Shee, Chandan; Singh, Tej P.; Kumar, Pravindra; Sharma, Ashwani K.

    2007-01-01

    A Kunitz-type trypsin inhibitor purified from the seeds of Murraya koenigii has been crystallized by the sitting-drop vapour-diffusion method using PEG 8000 as the precipitating agent. The crystals belong to the tetragonal space group P43212, with unit-cell parameters a = b = 75.8, c = 150.9 Å. The crystals contain two molecules in the asymmetric unit with a V M value of 2.5 Å3 Da−1. Diffraction was observed to 2.65 Å resolution and a complete data set was collected to 2.9 Å resolution. PMID:17401205

  11. Synthesis and single crystal x-ray diffraction study of a Schiff base derived from 4-acylpyrazolone and 2-aminophenol

    Energy Technology Data Exchange (ETDEWEB)

    Sharma, Naresh; Kant, Rajni, E-mail: vivek-gupta2k2@hotmail.com; Gupta, Vivek K., E-mail: vivek-gupta2k2@hotmail.com [Department of Physics and Electronics, University of Jammu, Jammu Tawi - 180006 (India); Jadeja, R. N. [Department of Chemistry, Faculty of Science, The M. S. University of Baroda, Vadodara-390002 (India)

    2014-04-24

    The title compound, (Z)-1-(3-chlorophenyl)-4[1((2hydroxyphenyl)amino)propylidene] -3-methyl-1H-pyrazol-5(4H)-one was synthesized by refluxing compound 1-(m-chlorophenyl)-3-methyl-4-propionyl-5-pyrazolone, with 2-aminophenol in ethanol. The compound crystallizes in the orthorhombic crystal system with space group Pca2{sub 1} having unit cell parameters: a = 26.2993(8), b = 7.0724(2) and c = 18.7170(5)Å. The structure contains two crystallographically independent molecules, A, and, B, in the asymmetric unit cell. The crystal structure was solved by direct method using single crystal X-ray diffraction data collected at room temperature and refined by full-matrix least-squares procedures to a final R- value of 0.049 for 5207 observed reflections.

  12. Crystal engineering on industrial diaryl pigments using lattice energy minimizations and X-ray powder diffraction.

    Science.gov (United States)

    Schmidt, Martin U; Dinnebier, Robert E; Kalkhof, Holger

    2007-08-23

    Diaryl azo pigments play an important role as yellow pigments for printing inks, with an annual pigment production of more than 50,000 t. The crystal structures of Pigment Yellow 12 (PY12), Pigment Yellow 13 (PY13), Pigment Yellow 14 (PY14), and Pigment Yellow 83 (PY83) were determined from X-ray powder data using lattice energy minimizations and subsequent Rietveld refinements. Details of the lattice energy minimization procedure and of the development of a torsion potential for the biphenyl fragment are given. The Rietveld refinements were carried out using rigid bodies, or constraints. It was also possible to refine all atomic positions individually without any constraint or restraint, even for PY12 having 44 independent non-hydrogen atoms per asymmetric unit. For PY14 (23 independent non-hydrogen atoms), additionally all atomic isotropic temperature factors could be refined individually. PY12 crystallized in a herringbone arrangement with twisted biaryl fragments. PY13 and PY14 formed a layer structure of planar molecules. PY83 showed a herringbone structure with planar molecules. According to quantum mechanical calculations, the twisting of the biaryl fragment results in a lower color strength of the pigments, whereas changes in the substitution pattern have almost no influence on the color strength of a single molecule. Hence, the experimentally observed lower color strength of PY12 in comparison with that of PY13 and PY83 can be explained as a pure packing effect. Further lattice energy calculations explained that the four investigated pigments crystallize in three different structures because these structures are the energetically most favorable ones for each compound. For example, for PY13, PY14, or PY83, a PY12-analogous crystal structure would lead to considerably poorer lattice energies and lower densities. In contrast, lattice energy calculations revealed that PY12 could adopt a PY13-type structure with only slightly poorer energy. This structure was

  13. Crystal Engineering on Industrial Diaryl Pigments Using Lattice Energy Minimizations and X-ray Powder Diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt,M.; Dinnebier, R.; Kalkhof, H.

    2007-01-01

    Diaryl azo pigments play an important role as yellow pigments for printing inks, with an annual pigment production of more than 50,000 t. The crystal structures of Pigment Yellow 12 (PY12), Pigment Yellow 13 (PY13), Pigment Yellow 14 (PY14), and Pigment Yellow 83 (PY83) were determined from X-ray powder data using lattice energy minimizations and subsequent Rietveld refinements. Details of the lattice energy minimization procedure and of the development of a torsion potential for the biphenyl fragment are given. The Rietveld refinements were carried out using rigid bodies, or constraints. It was also possible to refine all atomic positions individually without any constraint or restraint, even for PY12 having 44 independent non-hydrogen atoms per asymmetric unit. For PY14 (23 independent non-hydrogen atoms), additionally all atomic isotropic temperature factors could be refined individually. PY12 crystallized in a herringbone arrangement with twisted biaryl fragments. PY13 and PY14 formed a layer structure of planar molecules. PY83 showed a herringbone structure with planar molecules. According to quantum mechanical calculations, the twisting of the biaryl fragment results in a lower color strength of the pigments, whereas changes in the substitution pattern have almost no influence on the color strength of a single molecule. Hence, the experimentally observed lower color strength of PY12 in comparison with that of PY13 and PY83 can be explained as a pure packing effect. Further lattice energy calculations explained that the four investigated pigments crystallize in three different structures because these structures are the energetically most favorable ones for each compound. For example, for PY13, PY14, or PY83, a PY12-analogous crystal structure would lead to considerably poorer lattice energies and lower densities. In contrast, lattice energy calculations revealed that PY12 could adopt a PY13-type structure with only slightly poorer energy. This structure was

  14. 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.

  15. Basic of X-ray diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Giacovazzo, C. [Bari Univ. (Italy). Dip. Geomineralogico

    1996-09-01

    The basic concepts of X-ray diffraction may be more easily understood if it is made preliminary use of a mathematical background. In these pages the authors will first define the delta function and its use for the representation of a lattice. Then the concepts of Fourier transform and convolution are given. At the end of this talk one should realize that a crystal is the convolution of the lattice with a function representing the content of the unit cell.

  16. Characterization of synthetic virgilite-petalite mixed crystals by thermoluminescence and X-ray diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Correcher, V., E-mail: v.correcher@ciemat.es [CIEMAT, Av. Complutense 22, 28040 Madrid (Spain); Gomez-Ros, J.M. [CIEMAT, Av. Complutense 22, 28040 Madrid (Spain); Garcia-Guinea, J.; Crespo-Feo, E. [Museo Nacional de Ciencias Naturales (CSIC), C/Jose Gutierrez Abascal 2, 28006 Madrid (Spain)

    2009-07-15

    This paper reports on the dose response and fading effect of the blue thermoluminescence (TL) emission of lithium-rich aluminosilicates (virgilite-petalite mixture) synthesized by sol-gel method and characterised by means of X-ray diffraction. This material could be potentially valid for dose assessment since: (i) it is sensitive to ionising radiation, (ii) the dose dependence in the range of 0.5-5 Gy exhibits an acceptable linearity and (iii) the stability of the TL signal, after four months of storage, shows an initial rapid decay (ca. 55%) maintaining similar relative intensities from 40 to 50 days onwards. The structure of the TL emission has been analysed by means of a computerized glow curve fitting method based on general order kinetics. The calculation of the trapping parameters of each of the four glow peaks appearing at 80, 95, 110 and 125 deg. C (i.e. trap depth in eV, E; frequency factor in s{sup -1}, s, and the order of kinetics, b) indicates that cannot be fitted to a typical first or second order kinetics; the estimated b values are between 1.1 and 1.8.

  17. Crystallization and preliminary X-ray diffraction studies of Murraya koenigii trypsin inhibitor

    Energy Technology Data Exchange (ETDEWEB)

    Shee, Chandan [Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247 667 (India); Singh, Tej P. [Department of Biophysics, All India Institute of Medical Sciences, New Delhi 100 029 (India); Kumar, Pravindra, E-mail: kumarfbs@iitr.ernet.in; Sharma, Ashwani K., E-mail: kumarfbs@iitr.ernet.in [Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247 667 (India)

    2007-04-01

    A Kunitz-type trypsin inhibitor purified from the seeds of Murraya koenigii has been crystallized by the sitting-drop vapour-diffusion method using PEG 8000 as the precipitating agent. A Kunitz-type trypsin inhibitor purified from the seeds of Murraya koenigii has been crystallized by the sitting-drop vapour-diffusion method using PEG 8000 as the precipitating agent. The crystals belong to the tetragonal space group P4{sub 3}2{sub 1}2, with unit-cell parameters a = b = 75.8, c = 150.9 Å. The crystals contain two molecules in the asymmetric unit with a V{sub M} value of 2.5 Å{sup 3} Da{sup −1}. Diffraction was observed to 2.65 Å resolution and a complete data set was collected to 2.9 Å resolution.

  18. 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.

  19. 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%.

  20. Assessment of the Stoichiometry of Multicomponent Crystals Using Only X-ray Powder Diffraction Data.

    Science.gov (United States)

    Maguire, Courtney K; Brunskill, Andrew P J

    2015-06-01

    Knowledge of the unit cell volume of a crystalline form and the expected space filling requirements of an API molecule can be used to determine if a crystalline material is likely to be multicomponent, such as a solvate, hydrate, salt, or a co-crystal. The unit cell information can be readily accessed from powder diffraction data alone utilizing powder indexing methodology. If the unit cell has additional space not likely attributable to the API entity, then there is either a void or another component within the crystal lattice. This "leftover" space can be used to determine the likely stoichiometry of the additional component. A simple approach for calculating the expected required volume for a given molecule within a crystal using an atom based additive approach will be discussed. Coupling this estimation with the actual unit cell volumes and space group information obtained from powder indexing allows for the rapid evaluation of the likely stoichiometry of multicomponent crystals using diffraction data alone. This approach is particularly useful for the early assessment of new phases during salt, co-crystal, and polymorph screening, and also for the characterization of stable and unstable solvates.

  1. About some practical aspects of X-ray diffraction : From single crystal to powders

    Energy Technology Data Exchange (ETDEWEB)

    Giacovazzo, C. [Bari Univ. (Italy). Dip. Geomineralogico

    1996-09-01

    An ideal polycrystalline material or power is an ensemble of a very large number of randomly oriented crystallites. It is shown the effect that this random orientation has on the diffraction of a specimen assumed to contain only one reciprocal lattice node. The most remarkable difference with the single-crystal case is that now must think of scattering vectors not as lying on discrete nodes of reciprocal lattice vectors, the distances from the single-crystal reciprocal lattice nodes to the origin of reciprocal space.

  2. 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.

  3. Preferred orientation of n-hexane crystallized in silicon nanochannels: A combined x-ray diffraction and sorption isotherm study

    CERN Document Server

    Henschel, Anke; Hofmann, Tommy; Knorr, Klaus; Huber, Patrick; 10.1103/PhysRevE.79.032601

    2009-01-01

    We present an x-ray diffraction study on n-hexane in tubular silicon channels of approximately 10 nm diameter both as a function of the filling fraction f of the channels and as a function of temperature. Upon cooling, confined n-hexane crystallizes in a triclinic phase typical of the bulk crystalline state. However, the anisotropic spatial confinement leads to a preferred orientation of the confined crystallites, where the crystallographic direction coincides with the long axis of the channels. The magnitude of this preferred orientation increases with the filling fraction, which corroborates the assumption of a Bridgman-type crystallization process being responsible for the peculiar crystalline texture. This growth process predicts for a channel-like confinement an alignment of the fastest crystallization direction parallel to the long channel axis. It is expected to be increasingly effective with the length of solidifying liquid parcels and thus with increasing f. In fact, the fastest solidification front...

  4. Expression, purification, crystallization and X-ray diffraction studies of the molecular chaperone prefoldin from Homo sapiens.

    Science.gov (United States)

    Aikawa, Yoshiki; Kida, Hiroshi; Nishitani, Yuichi; Miki, Kunio

    2015-09-01

    Proper protein folding is an essential process for all organisms. Prefoldin (PFD) is a molecular chaperone that assists protein folding by delivering non-native proteins to group II chaperonin. A heterohexamer of eukaryotic PFD has been shown to specifically recognize and deliver non-native actin and tubulin to chaperonin-containing TCP-1 (CCT), but the mechanism of specific recognition is still unclear. To determine its crystal structure, recombinant human PFD was reconstituted, purified and crystallized. X-ray diffraction data were collected to 4.7 Å resolution. The crystals belonged to space group P21212, with unit-cell parameters a = 123.2, b = 152.4, c = 105.9 Å.

  5. Crystallization in Fe- and Co-Based Amorphous Alloys Studied by In-Situ X-Ray Diffraction

    Science.gov (United States)

    Zhang, L. J.; Yu, P. F.; Cheng, H.; Zhang, M. D.; Liu, D. J.; Zhou, Z.; Jin, Q.; Liaw, P. K.; Li, G.; Liu, R. P.

    2016-12-01

    The amorphous alloys, Fe80Si20, Fe78Si9B13, and Fe4Co67Mo1.5Si16.5B11, were prepared by the spinning method in pure argon. The crystallization behaviors of the three amorphous alloys were researched by in-situ X-ray diffraction (XRD), and the crystallization activation energy was calculated, based on the results of differential scanning calorimetry. The crystallization mechanism of the Fe- and Co-based alloys was analyzed, based on the experimental data. The transformation kinetics was described in terms of Johnson-Mehl-Avrami kinetics, except that the Avrami exponent of the Fe78Si9B13 amorphous alloy annealed at 753 K (480 °C) was 4.12; the obtained values for the overall Avrami exponents of the other three amorphous alloys were below 1, as usually found for the Fe-Si amorphous alloys.

  6. 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.

  7. Diffractive X-Ray Telescopes

    Science.gov (United States)

    Skinner, Gerald K.

    2010-01-01

    Diffractive X-ray telescopes, using zone plates, phase Fresnel lenses, or related optical elements have the potential to provide astronomers with true imaging capability with resolution many orders of magnitude better than available in any other waveband. Lenses that would be relatively easy to fabricate could have an angular resolution of the order of micro-arc-seconds or even better, that would allow, for example, imaging of the distorted spacetime in the immediate vicinity of the super-massive black holes in the center of active galaxies. What then is precluding their immediate adoption? Extremely long focal lengths, very limited bandwidth, and difficulty stabilizing the image are the main problems. The history, and status of the development of such lenses is reviewed here and the prospects for managing the challenges that they present are discussed.

  8. Diffractive X-ray Telescopes

    CERN Document Server

    Skinner, Gerald K

    2010-01-01

    Diffractive X-ray telescopes using zone plates, phase Fresnel lenses, or related optical elements have the potential to provide astronomers with true imaging capability with resolution several orders of magnitude better than available in any other waveband. Lenses that would be relatively easy to fabricate could have an angular resolution of the order of micro-arc-seconds or even better, that would allow, for example, imaging of the distorted space- time in the immediate vicinity of the super-massive black holes in the center of active galaxies What then is precluding their immediate adoption? Extremely long focal lengths, very limited bandwidth, and difficulty stabilizing the image are the main problems. The history, and status of the development of such lenses is reviewed here and the prospects for managing the challenges that they present are discussed.

  9. Crystallization and X-ray diffraction studies of a complete bacterial fatty-acid synthase type I

    Energy Technology Data Exchange (ETDEWEB)

    Enderle, Mathias [Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main (Germany); Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried (Germany); McCarthy, Andrew [EMBL Grenoble, 71 Avenue des Martyrs, 38042 Grenoble CEDEX 9 (France); Paithankar, Karthik Shivaji, E-mail: paithankar@em.uni-frankfurt.de [Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main (Germany); Grininger, Martin, E-mail: paithankar@em.uni-frankfurt.de [Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main (Germany); Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried (Germany)

    2015-10-23

    Bacterial and fungal type I fatty-acid synthases (FAS I) are evolutionarily connected, as bacterial FAS I is considered to be the ancestor of fungal FAS I. In this work, the production, crystallization and X-ray diffraction data analysis of a bacterial FAS I are reported. While a deep understanding of the fungal and mammalian multi-enzyme type I fatty-acid synthases (FAS I) has been achieved in recent years, the bacterial FAS I family, which is narrowly distributed within the Actinomycetales genera Mycobacterium, Corynebacterium and Nocardia, is still poorly understood. This is of particular relevance for two reasons: (i) although homologous to fungal FAS I, cryo-electron microscopic studies have shown that bacterial FAS I has unique structural and functional properties, and (ii) M. tuberculosis FAS I is a drug target for the therapeutic treatment of tuberculosis (TB) and therefore is of extraordinary importance as a drug target. Crystals of FAS I from C. efficiens, a homologue of M. tuberculosis FAS I, were produced and diffracted X-rays to about 4.5 Å resolution.

  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 studies of a catechol-O-methyltransferase/inhibitor complex

    Energy Technology Data Exchange (ETDEWEB)

    Rodrigues, M. L. [Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa, Av. República, Apt. 127, 2781-901 Oeiras (Portugal); Bonifácio, M. J.; Soares-da-Silva, P. [Department of Research and Development, BIAL, 4785 S. Mamede do Coronado (Portugal); Carrondo, M. A.; Archer, M., E-mail: archer@itqb.unl.pt [Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa, Av. República, Apt. 127, 2781-901 Oeiras (Portugal)

    2005-01-01

    Catechol-O-methyltransferase has been co-crystallized with a novel inhibitor, which has potential therapeutic application in the Parkinson’s disease therapy. Inhibitors of the enzyme catechol-O-methyltransferase (COMT) are used as co-adjuvants in the therapy of Parkinson’s disease. A recombinant form of the soluble cytosolic COMT from rat has been co-crystallized with a new potent inhibitor, BIA 8-176 [(3,4-dihydroxy-2-nitrophenyl)phenylmethanone], by the vapour-diffusion method using PEG 6K as precipitant. Crystals diffract to 1.6 Å resolution on a synchrotron-radiation source and belong to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 52.77, b = 79.63, c = 61.54 Å, β = 91.14°.

  12. 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.

  13. X-rays diffraction on a new chromium oxide single-crystal thin film prepared by molecular beam epitaxy

    NARCIS (Netherlands)

    Du, X. S.; Hak, S.; Hibma, T.; Rogojanu, O. C.; Struth, B.

    2006-01-01

    Chromium oxide films were prepared on MgO substrates by molecular beam epitaxy. The crystalline structure of the films was characterized by X-ray diffraction (XRD) with conventional as well as synchrotron X-ray sources. The theta-2 theta spectra showed that the film was a new chromium oxide epitaxia

  14. X-rays diffraction on a new chromium oxide single-crystal thin film prepared by molecular beam epitaxy

    NARCIS (Netherlands)

    Du, X. S.; Hak, S.; Hibma, T.; Rogojanu, O. C.; Struth, B.

    2006-01-01

    Chromium oxide films were prepared on MgO substrates by molecular beam epitaxy. The crystalline structure of the films was characterized by X-ray diffraction (XRD) with conventional as well as synchrotron X-ray sources. The theta-2 theta spectra showed that the film was a new chromium oxide

  15. Crystallization and preliminary X-ray diffraction studies of l-rhamnose isomerase from Pseudomonas stutzeri

    Energy Technology Data Exchange (ETDEWEB)

    Yoshida, Hiromi [Molecular Structure Research Group, Information Technology Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793 (Japan); Wayoon, Poonperm; Takada, Goro; Izumori, Ken [Department of Biochemistry and Food Science, Faculty of Agriculture and Rare Sugar Research Center, Kagawa University, Miki-cho, Kagawa 761-0795 (Japan); Kamitori, Shigehiro, E-mail: kamitori@med.kagawa-u.ac.jp [Molecular Structure Research Group, Information Technology Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793 (Japan)

    2006-06-01

    Recombinant l-rhamnose isomerase from P. stutzeri has been crystallized. Diffraction data have been collected to 2.0 Å resolution. l-Rhamnose isomerase from Pseudomonas stutzeri (P. stutzeril-RhI) catalyzes not only the reversible isomerization of l-rhamnose to l-rhamnulose, but also isomerization between various rare aldoses and ketoses. Purified His-tagged P. stutzeril-RhI was crystallized by the hanging-drop vapour-diffusion method. The crystals belong to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 74.3, b = 104.0, c = 107.0 Å, β = 106.8°. Diffraction data have been collected to 2.0 Å resolution. The molecular weight of the purified P. stutzeril-RhI with a His tag at the C-terminus was confirmed to be 47.7 kDa by MALDI–TOF mass-spectrometric analysis and the asymmetric unit is expected to contain four molecules.

  16. Crystallization and preliminary X-ray diffraction studies of the glutaminyl cyclase from Carica papaya latex

    Energy Technology Data Exchange (ETDEWEB)

    Azarkan, Mohamed [Laboratoire de Chimie Générale I, Faculté de Médecine-ULB CP609, 808 Route de Lennik, B-1070 Brussels (Belgium); Clantin, Bernard; Bompard, Coralie [CNRS-UMR 8525, Institut de Biologie de Lille, BP 477, 1 Rue du Professeur Calmette, F-59021 Lille (France); Belrhali, Hassan [EMBL Grenoble Outstation, 6 Rue Jules Horowitz, BP 181, F-38042 Grenoble CEDEX 9 (France); Baeyens-Volant, Danielle [Laboratoire de Chimie Générale I, Faculté de Médecine-ULB CP609, 808 Route de Lennik, B-1070 Brussels (Belgium); Looze, Yvan [Laboratoire de Chimie Générale, Institut de Pharmacie-ULB CP206/04, Boulevard du Triomphe, B-1050 Brussels (Belgium); Villeret, Vincent, E-mail: vincent.villeret@ibl.fr [CNRS-UMR 8525, Institut de Biologie de Lille, BP 477, 1 Rue du Professeur Calmette, F-59021 Lille (France); Wintjens, René, E-mail: vincent.villeret@ibl.fr [Laboratoire de Chimie Générale, Institut de Pharmacie-ULB CP206/04, Boulevard du Triomphe, B-1050 Brussels (Belgium); Laboratoire de Chimie Générale I, Faculté de Médecine-ULB CP609, 808 Route de Lennik, B-1070 Brussels (Belgium)

    2005-01-01

    The glutaminyl cyclase isolated from C. papaya latex has been crystallized using the hanging-drop method. Diffraction data have been collected at ESRF beamline BM14 and processed to 1.7 Å resolution. In living systems, the intramolecular cyclization of N-terminal glutamine residues is accomplished by glutaminyl cyclase enzymes (EC 2.3.2.5). While in mammals these enzymes are involved in the synthesis of hormonal and neurotransmitter peptides, the physiological role played by the corresponding plant enzymes still remains to be unravelled. Papaya glutaminyl cyclase (PQC), a 33 kDa enzyme found in the latex of the tropical tree Carica papaya, displays an exceptional resistance to chemical and thermal denaturation as well as to proteolysis. In order to elucidate its enzymatic mechanism and to gain insights into the structural determinants underlying its remarkable stability, PQC was isolated from papaya latex, purified and crystallized by the hanging-drop vapour-diffusion method. The crystals belong to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 62.82, b = 81.23, c = 108.17 Å and two molecules per asymmetric unit. Diffraction data have been collected at ESRF beamline BM14 and processed to a resolution of 1.7 Å.

  17. Purification, crystallization and preliminary X-ray diffraction of human S100A15

    Energy Technology Data Exchange (ETDEWEB)

    Boeshans, Karen M. [X-ray Crystallography Facility, NIAMS, National Institutes of Health, Bethesda, MD 20892 (United States); Wolf, Ronald; Voscopoulos, Christopher [Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 (United States); Gillette, William; Esposito, Dominic [Protein Expression Laboratory, Research Technology Program, National Cancer Institute, SAIC-Frederick Inc., Frederick, MD 21702 (United States); Mueser, Timothy C. [Department of Chemistry, University of Toledo, Toledo, OH 43606 (United States); Yuspa, Stuart H. [Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 (United States); Ahvazi, Bijan, E-mail: ahvazib@mail.nih.gov [X-ray Crystallography Facility, NIAMS, National Institutes of Health, Bethesda, MD 20892 (United States)

    2006-05-01

    S100 proteins are differentially expressed during epithelial cell maturation, tumorigenesis and inflammation. The novel human S100A15 protein has been cloned, expressed, purified and crystallized in two crystal forms, a triclinic and a monoclinic form, which diffract to 1.7 and 2.0 Å, respectively. Human S100A15 is a novel member of the S100 family of EF-hand calcium-binding proteins and was recently identified in psoriasis, where it is significantly upregulated in lesional skin. The protein is implicated as an effector in calcium-mediated signal transduction pathways. Although its biological function is unclear, the association of the 11.2 kDa S100A15 with psoriasis suggests that it contributes to the pathogenesis of the disease and could provide a molecular target for therapy. To provide insight into the function of S100A15, the protein was crystallized to visualize its structure and to further the understanding of how the many similar calcium-binding mediator proteins in the cell distinguish their cognate target molecules. The S100A15 protein has been cloned, expressed and purified to homogeneity and produced two crystal forms. Crystals of form I are triclinic, with unit-cell parameters a = 33.5, b = 44.3, c = 44.8 Å, α = 71.2, β = 68.1, γ = 67.8° and an estimated two molecules in the asymmetric unit, and diffract to 1.7 Å resolution. Crystals of form II are monoclinic, with unit-cell parameters a = 82.1, b = 33.6, c = 52.2 Å, β = 128.2° and an estimated one molecule in the asymmetric unit, and diffract to 2.0 Å resolution. This structural analysis of the human S100A15 will further aid in the phylogenic comparison between the other members of the S100 protein family, especially the highly homologous paralog S100A7.

  18. Glancing angle synchrotron X-ray diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Cernik, R.J. [Daresbury Lab., Warrington, WA (United States)

    1996-09-01

    This paper describes in basic detail some of the techniques that can be used to study thin films and surfaces. These are all in the X-ray region and cover reflectivity, diffraction form polycrystalline films, textured films and single crystal films. Other effects such as fluorescence and diffuse scattering are mentioned but not discussed in detail. Two examples of the reflectivity from multilayers and the diffraction from iron oxide films are discussed. The advantages of the synchrotron for these studies is stressed and the experimental geometries that can be employed are described i detail. A brief bibliography is provided at the end to accompany this part of the 1996 Frascati school.

  19. 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.

  20. Overexpression, purification, crystallization and preliminary X-ray diffraction of the nisin resistance protein from Streptococcus agalactiae.

    Science.gov (United States)

    Khosa, Sakshi; Hoeppner, Astrid; Kleinschrodt, Diana; Smits, Sander H J

    2015-06-01

    Nisin is a 34-amino-acid antimicrobial peptide produced by Lactococcus lactis belonging to the class of lantibiotics. Nisin displays a high bactericidal activity against various Gram-positive bacteria, including some human-pathogenic strains. However, there are some nisin-non-producing strains that are naturally resistant owing to the presence of the nsr gene within their genome. The encoded protein, NSR, cleaves off the last six amino acids of nisin, thereby reducing its bactericidal efficacy. An expression and purification protocol has been established for the NSR protein from Streptococcus agalactiae COH1. The protein was successfully crystallized using the vapour-diffusion method in hanging and sitting drops, resulting in crystals that diffracted X-rays to 2.8 and 2.2 Å, respectively.

  1. 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).

  2. 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.

  3. Building X-ray Diffraction Calibration Software

    Energy Technology Data Exchange (ETDEWEB)

    Lande, Joshua; /Marlboro Coll.

    2007-10-31

    X-ray diffraction is a technique used to analyze the structure of crystals. It records the interference pattern created when x-rays travel through a crystal. Three dimensional structure can be inferred from these two dimensional diffraction patterns. Before the patterns can be analyzed, diffraction data must be precisely calibrated. Calibration is used to determine the experimental parameters of the particular experiment. This is done by fitting the experimental parameters to the diffraction pattern of a well understood crystal. Fit2D is a software package commonly used to do this calibration but it leaves much to be desired. In particular, it does not give very much control over the calibration of the data, requires a significant amount of manual input, does not allow for the calibration of highly tilted geometries, does not properly explain the assumptions that it is making, and cannot be modified. We build code to do this calibration while at the same time overcoming the limitations of Fit2D. This paper describes the development of the calibration software and the assumptions that are made in doing the calibration.

  4. 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.

  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. The application of eigensymmetries of face forms to X-ray diffraction intensities of crystals twinned by 'reticular merohedry'.

    Science.gov (United States)

    Klapper, H; Hahn, Th

    2012-01-01

    This paper is an extension of a previous treatment of `twins by merohedry' with full lattice coincidence [Σ = 1, Klapper & Hahn (2010). Acta Cryst. A66, 327-346] to `twins by reticular merohedry' with partial lattice coincidence (Σ > 1). Again, the sets of symmetrically equivalent reflections {hkl} are considered as sets of equivalent faces (face forms) {hkl}, and the behaviour of the oriented eigensymmetries of these forms under the action of a twin operation is used to determine the X-ray reflection sets, the intensities of which are affected or not affected by the twinning. The following cases are treated: rhombohedral obverse/reverse Σ3 twins, cubic Σ3 (spinel) twins, tetragonal Σ5 twins (twin elements m'(120), 2'[ ̅210]) and hexagonal Σ7 twins (m'(12 ̅30), 2'[2 ̅10]). For each case the twin laws for all relevant point groups are defined, and the twin diffraction cases A (intensity of twin-related reflection sets not affected), B1 (intensity affected), B2 (intensity affected only by anomalous scattering) and S (single, i.e. non-coincident reflection sets) are derived for all twin laws. A special treatment is provided for the cubic Σ3 twins, where the cubic face forms first have to be split into up to four rhombohedral subforms with a threefold axis along one of the four cube directions, here [111]. These subforms exhibit different twin diffraction cases analogous to those derived for the rhombohedral obverse/reverse Σ3 twins. A complete list of the split forms and their diffraction cases for all cubic point groups and all Σ3 twin elements is given. The application to crystal structure determination of crystals twinned by reticular merohedry and to X-ray topographic mapping of twin domains is discussed.

  7. Crystallization and X-ray diffraction studies of crustacean proliferating cell nuclear antigen

    Science.gov (United States)

    Carrasco-Miranda, Jesus S.; Cardona-Felix, Cesar S.; Lopez-Zavala, Alonso A.; de-la-Re-Vega, Enrique; De la Mora, Eugenio; Rudiño-Piñera, Enrique; Sotelo-Mundo, Rogerio R.; Brieba, Luis G.

    2012-01-01

    Proliferating cell nuclear antigen (PCNA), a member of the sliding clamp family of proteins, interacts specifically with DNA replication and repair proteins through a small peptide motif called the PCNA-interacting protein or PIP box. PCNA is recognized as one of the key proteins involved in DNA metabolism. In the present study, the recombinant PCNA from Litopenaeus vannamei (LvPCNA) was heterologously overexpressed and purified using metal ion-affinity chromatography. Crystals suitable for diffraction grew overnight using the hanging-drop vapour-diffusion method. LvPCNA crystals belong to space group C2 with unit-cell parameters a = 144.6, b = 83.4, c = 74.3 Å, β = 117.6°. One data set was processed to 3 Å resolution, with an overall R meas of 0.09 and a completeness of 93.3%. Initial phases were obtained by molecular replacement using a homology model of LvPCNA as the search model. Refinement and structural analysis are underway. This report is the first successful crystallographic analysis of a marine crustacean decapod shrimp (L. vannamei) proliferating cell nuclear antigen. PMID:23143251

  8. Crystal structure of pentasodium hydrogen dicitrate from synchrotron X-ray powder diffraction data and DFT comparison

    Energy Technology Data Exchange (ETDEWEB)

    Rammohan, Alagappa; Kaduk, James A.

    2017-01-27

    The crystal structure of pentasodium hydrogen dicitrate, Na5H(C6H5O7)2, has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Each of the two independent citrate anions is joined into a dimer by very strong centrosymmetric O—H...O hydrogen bonds, with O...O distances of 2.419 and 2.409 Å. Four octahedrally coordinated Na+ions share edges to form open layers parallel to theabplane. A fifth Na+ion in trigonal–bipyramidal coordination shares faces with NaO6octahedra on both sides of these layers.

  9. Crystal structure of dirubidium hydrogen citrate from laboratory X-ray powder diffraction data and DFT comparison.

    Science.gov (United States)

    Rammohan, Alagappa; Kaduk, James A

    2017-01-01

    The crystal structure of dirubidium hydrogen citrate, 2Rb(+)·HC6H5O7(2-), has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The un-ionized carb-oxy-lic acid group forms helical chains of very strong hydrogen bonds (O⋯O ∼ 2.42 Å) along the b axis. The hy-droxy group participates in a chain of intra- and inter-molecular hydrogen bonds along the c axis. These hydrogen bonds result in corrugated hydrogen-bonded layers in the bc plane. The Rb(+) cations are six-coordinate, and share edges and corners to form layers in the ab plane. The inter-layer contacts are composed of the hydro-phobic methyl-ene groups.

  10. Crystal structure of caesium di-hydrogen citrate from laboratory X-ray powder diffraction data and DFT comparison.

    Science.gov (United States)

    Rammohan, Alagappa; Kaduk, James A

    2017-02-01

    The crystal structure of caesium di-hydrogen citrate, Cs(+)·H2C6H5O7(-), has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The coordination polyhedra of the nine-coordinate Cs(+) cations share edges to form chains along the a-axis. These chains are linked by corners along the c-axis. The un-ionized carb-oxy-lic acid groups form two different types of hydrogen bonds; one forms a helical chain along the c-axis, and the other is discrete. The hy-droxy group participates in both intra- and inter-molecular hydrogen bonds.

  11. Crystal structure of penta­sodium hydrogen dicitrate from synchrotron X-ray powder diffraction data and DFT comparison

    Science.gov (United States)

    Kaduk, James A.

    2017-01-01

    The crystal structure of penta­sodium hydrogen dicitrate, Na5H(C6H5O7)2, has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Each of the two independent citrate anions is joined into a dimer by very strong centrosymmetric O—H⋯O hydrogen bonds, with O⋯O distances of 2.419 and 2.409 Å. Four octa­hedrally coordinated Na+ ions share edges to form open layers parallel to the ab plane. A fifth Na+ ion in trigonal–bipyramidal coordination shares faces with NaO6 octahedra on both sides of these layers. PMID:28217360

  12. Crystal structure of trirubidium citrate monohydrate from laboratory X-ray powder diffraction data and DFT comparison

    Science.gov (United States)

    Kaduk, James A.

    2017-01-01

    The crystal structure of the title compound, 3Rb+·C6H5O7 3−·H2O, has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The hy­droxy group participates in an intra­molecular hydrogen bond to the deprotonated central carboxyl­ate group with graph-set motif S(5). The water mol­ecule acts as a hydrogen-bond donor to both terminal and central carboxyl­ate O atoms. The three independent rubidium cations are seven-, six- and six-coordinate, with bond-valence sums of 0.84, 1.02, and 0.95, respectively. In the extended structure, their polyhedra share edges and corners to form a three-dimensional network. The hydro­phobic methyl­ene groups occupy channels along the b axis. PMID:28217348

  13. 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.

  14. Purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies of great cormorant (Phalacrocorax carbo) haemoglobin

    Energy Technology Data Exchange (ETDEWEB)

    Jagadeesan, G. [Presidency College, Chennai 600 005 (India); Malathy, P.; Gunasekaran, K. [University of Madras, Chennai 600 025 (India); Harikrishna Etti, S. [GKM College of Engineering and Technology, Kamaraj Salai, Chennai 600 063 (India); Aravindhan, S., E-mail: aravindhanpresidency@gmail.com [Presidency College, Chennai 600 005 (India)

    2014-10-25

    The great cormorant hemoglobin has been isolated, purified and crystallized and the three dimensional structure is solved using molecular replacement technique. Haemoglobin is the iron-containing oxygen-transport metalloprotein that is present in the red blood cells of all vertebrates. In recent decades, there has been substantial interest in attempting to understand the structural basis and functional diversity of avian haemoglobins. Towards this end, purification, crystallization, preliminary X-ray diffraction and molecular-replacement studies have been carried out on cormorant (Phalacrocorax carbo) haemoglobin. Crystals were grown by the hanging-drop vapour-diffusion method using PEG 3350, NaCl and glycerol as precipitants. The crystals belonged to the trigonal system P3{sub 1}21, with unit-cell parameters a = b = 55.64, c = 153.38 Å, β = 120.00°; a complete data set was collected to a resolution of 3.5 Å. Matthews coefficient analysis indicated that the crystals contained a half-tetramer in the asymmetric unit.

  15. First spin-resolved electron distributions in crystals from combined polarized neutron and X-ray diffraction experiments

    Directory of Open Access Journals (Sweden)

    Maxime Deutsch

    2014-05-01

    Full Text Available Since the 1980s it has been possible to probe crystallized matter, thanks to X-ray or neutron scattering techniques, to obtain an accurate charge density or spin distribution at the atomic scale. Despite the description of the same physical quantity (electron density and tremendous development of sources, detectors, data treatment software etc., these different techniques evolved separately with one model per experiment. However, a breakthrough was recently made by the development of a common model in order to combine information coming from all these different experiments. Here we report the first experimental determination of spin-resolved electron density obtained by a combined treatment of X-ray, neutron and polarized neutron diffraction data. These experimental spin up and spin down densities compare very well with density functional theory (DFT calculations and also confirm a theoretical prediction made in 1985 which claims that majority spin electrons should have a more contracted distribution around the nucleus than minority spin electrons. Topological analysis of the resulting experimental spin-resolved electron density is also briefly discussed.

  16. In situ X-ray diffraction study of crystallization process of GeSbTe thin films during heat treatment

    Energy Technology Data Exchange (ETDEWEB)

    Kato, Naohiko [Toyota Central R and D Labs., Inc., Nagakute, Aichi 480-1192 (Japan)]. E-mail: e0957@mosk.tytlabs.co.jp; Konomi, Ichiro [Toyota Central R and D Labs., Inc., Nagakute, Aichi 480-1192 (Japan); Seno, Yoshiki [Toyota Central R and D Labs., Inc., Nagakute, Aichi 480-1192 (Japan); Motohiro, Tomoyoshi [Toyota Central R and D Labs., Inc., Nagakute, Aichi 480-1192 (Japan)

    2005-05-15

    The crystallization processes of the Ge{sub 2}Sb{sub 2}Te{sub 5} thin film used for PD and DVD-RAM were studied in its realistic optical disk film configurations for the first time by X-ray diffraction using an intense X-ray beam of a synchrotron orbital radiation facility (SPring-8) and in situ quick detection with a Position-Sensitive-Proportional-Counter. The dependence of the amorphous-to-fcc phase-change temperature T{sub 1} on the rate of temperature elevation R{sub et} gave an activation energy E{sub a}: 0.93 eV much less than previously reported 2.2 eV obtained from a model sample 25-45 times thicker than in the real optical disks. The similar measurement on the Ge{sub 4}Sb{sub 1}Te{sub 5} film whose large reflectance change attains the readability by CD-ROM drives gave E{sub a}: 1.13 eV with larger T{sub 1} than Ge{sub 2}Sb{sub 2}Te{sub 5} thin films at any R{sub et} implying a lower sensitivity in erasing as well as a better data stability of the phase-change disk.

  17. Solid state characterization and crystal structure from X-ray powder diffraction of two polymorphic forms of ranitidine base.

    Science.gov (United States)

    de Armas, Héctor Novoa; Peeters, Oswald M; Blaton, Norbert; Van Gyseghem, Elke; Martens, Johan; Van Haele, Gerrit; Van Den Mooter, Guy

    2009-01-01

    Ranitidine hydrochloride (RAN-HCl), a known anti-ulcer drug, is the product of reaction between HCl and ranitidine base (RAN-B). RAN-HCl has been extensively studied; however this is not the case of the RAN-B. The solid state characterization of RAN-B polymorphs has been carried out using different analytical techniques (microscopy, thermal analysis, Fourier transform infrared spectrometry in the attenuated total reflection mode, (13)C-CPMAS-NMR spectroscopy and X-ray powder diffraction). The crystal structures of RAN-B form I and form II have been determined using conventional X-ray powder diffraction in combination with simulated annealing and whole profile pattern matching, and refined using rigid-body Rietveld refinement. RAN-B form I is a monoclinic polymorph with cell parameters: a = 7.317(2), b = 9.021(2), c = 25.098(6) A, beta = 95.690(1) degrees and space group P2(1)/c. The form II is orthorhombic: a = 31.252(4), b = 13.052(2), c = 8.0892(11) A with space group Pbca. In RAN-B polymorphs, the nitro group is involved in a strong intramolecular hydrogen bond responsible for the existence of a Z configuration in the enamine portion of the molecules. A tail to tail packing motif can be denoted via intermolecular hydrogen bonds. The crystal structures of RAN-B forms are compared to those of RAN-HCl polymorphs. RAN-B polymorphs are monotropic polymorphic pairs.

  18. On diffraction and absorption of X-rays in perfect crystals

    OpenAIRE

    Morelhao, Sergio L.; Avanci, Luis H.

    2005-01-01

    This work reports the incompatibility of the Stokes relation for time reversibility of wave's propagation and the usage of complex atomic form-factor in diffraction theories. The implications behind a diffraction theory that obeys the Stokes relation is discussed.

  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. Study on the Crystallization of Amorphous Cr-Si-Ni Thin Films Using in situ X-ray Diffraction

    Institute of Scientific and Technical Information of China (English)

    Xianping DONG; Jiansheng WU

    2001-01-01

    Crystallization behavior of amorphous Cr-Si-Ni thin films was investigated by means of high temperature in situ X-ray diffraction measurements. The diffraction spectra were recorded isothermally at temperature between 250 and 750℃. The in situ testing of crystallization enables the direct observation of structure evolution which is dependent on heat treatment.Based on the testing results, the grain sizes of the crystalline phases were compared and phase transition tendency was understood. In the mean time, electrical properties of the films as functions of annealing temperature and time have been studied. The increase of volume fraction of CrSi2 crystallinc phases in the Cr-Si-Ni films leads to the decrease in conductivity of the films.The annealing behavior of temperature coefficient of resistance (TCR) is a result of competition between a negative contribution caused by the weak localization effects in amorphous region and a positive contribution caused by CrSi2 grains. Thus the proper mixture of amorphous and crystalline constituents could result in a final zero TCR.

  1. High-resolution X-ray diffraction studies of multilayers

    DEFF Research Database (Denmark)

    Christensen, Finn Erland; Hornstrup, Allan; Schnopper, H. W.

    1988-01-01

    High-resolution X-ray diffraction studies of the perfection of state-of-the-art multilayers are presented. Data were obtained using a triple-axis perfect-crystal X-ray diffractometer. Measurements reveal large-scale figure errors in the substrate. A high-resolution triple-axis set up is required...

  2. Synchrotron x-ray diffraction study of liquid surfaces

    DEFF Research Database (Denmark)

    Als-Nielsen, Jens Aage; Pershan, P.S.

    1983-01-01

    A spectrometer for X-ray diffraction and refraction studies of horizontal, free surfaces of liquids is described. As an illustration smetic-A layering at the surface of a liquid crystal is presented.......A spectrometer for X-ray diffraction and refraction studies of horizontal, free surfaces of liquids is described. As an illustration smetic-A layering at the surface of a liquid crystal is presented....

  3. Synchrotron x-ray diffraction study of liquid surfaces

    DEFF Research Database (Denmark)

    Als-Nielsen, Jens Aage; Pershan, P.S.

    1983-01-01

    A spectrometer for X-ray diffraction and refraction studies of horizontal, free surfaces of liquids is described. As an illustration smetic-A layering at the surface of a liquid crystal is presented.......A spectrometer for X-ray diffraction and refraction studies of horizontal, free surfaces of liquids is described. As an illustration smetic-A layering at the surface of a liquid crystal is presented....

  4. 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.

  5. Crystal structure of CuFe{sub 2}InSe{sub 4} from X-ray powder diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Delgado, G.E. [Laboratorio de Cristalografia, Departamento de Quimica, Facultad de Ciencias, Universidad de Los Andes, Merida 5101 (Venezuela)], E-mail: gerzon@ula.ve; Mora, A.J. [Laboratorio de Cristalografia, Departamento de Quimica, Facultad de Ciencias, Universidad de Los Andes, Merida 5101 (Venezuela); Grima-Gallardo, P.; Quintero, M. [Centro de Estudio de Semiconductores, Departamento de Fisica, Facultad de Ciencias, Universidad de Los Andes, Merida 5101 (Venezuela)

    2008-04-24

    The crystal structure of the semiconductor compound CuFe{sub 2}InSe{sub 4} was analyzed using X-ray powder diffraction data. The powder pattern refined by the Rietveld method was composed of 86.6% of the principal phase CuFe{sub 2}InSe{sub 4} and 13.4% of the binary phase FeSe. CuFe{sub 2}InSe{sub 4} crystallizes in the tetragonal space group I4-bar2m (no. 121), Z = 2, with unit cell parameters a = 5.7694(3) A, c = 11.495(1) A, V = 382.62(4) A{sup 3}. FeSe crystallizes in the tetragonal space group P4/nmm (no. 129), Z = 2, and a = 3.784(1) A, c 5.502(2) A, V = 78.78(4) A{sup 3}. The refinement of 28 instrumental and structural parameters led to R{sub p} = 8.2%, R{sub wp} = 10.7%, R{sub exp} = 6.7% and S = 1.7; R{sub B} = 9.9% (CuFe{sub 2}InSe{sub 4}), R{sub B} = 8.8% (FeSe) for 76 and 36 independent reflections, respectively.

  6. 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.

  7. X-Ray Diffractive Optics

    Science.gov (United States)

    Dennis, Brian; Li, Mary; Skinner, Gerald

    2013-01-01

    X-ray optics were fabricated with the capability of imaging solar x-ray sources with better than 0.1 arcsecond angular resolution, over an order of magnitude finer than is currently possible. Such images would provide a new window into the little-understood energy release and particle acceleration regions in solar flares. They constitute one of the most promising ways to probe these regions in the solar atmosphere with the sensitivity and angular resolution needed to better understand the physical processes involved. A circular slit structure with widths as fine as 0.85 micron etched in a silicon wafer 8 microns thick forms a phase zone plate version of a Fresnel lens capable of focusing approx. =.6 keV x-rays. The focal length of the 3-cm diameter lenses is 100 microns, and the angular resolution capability is better than 0.1 arcsecond. Such phase zone plates were fabricated in Goddard fs Detector Development Lab. (DDL) and tested at the Goddard 600-microns x-ray test facility. The test data verified that the desired angular resolution and throughput efficiency were achieved.

  8. Two-dimensional x-ray diffraction

    CERN Document Server

    He, Bob B

    2009-01-01

    Written by one of the pioneers of 2D X-Ray Diffraction, this useful guide covers the fundamentals, experimental methods and applications of two-dimensional x-ray diffraction, including geometry convention, x-ray source and optics, two-dimensional detectors, diffraction data interpretation, and configurations for various applications, such as phase identification, texture, stress, microstructure analysis, crystallinity, thin film analysis and combinatorial screening. Experimental examples in materials research, pharmaceuticals, and forensics are also given. This presents a key resource to resea

  9. Crystal structure of CuFeInSe{sub 3} from X-ray powder diffraction data

    Energy Technology Data Exchange (ETDEWEB)

    Mora, Asiloe J.; Delgado, Gerzon E. [Laboratorio de Cristalografia, Departamento de Quimica, Facultad de Ciencias, Universidad de Los Andes, Merida 5101 (Venezuela); Grima-Gallardo, Pedro [Centro de Estudios de Semiconductores, Departamento de Fisica, Facultad de Ciencias, Universidad de Los Andes, Merida 5101 (Venezuela)

    2007-02-15

    The crystal structure of the adamantane compound CuFeInSe{sub 3}, belonging to the system (CuInSe{sub 2}){sub 1-x}(FeSe){sub x} with x=0.5, was analyzed using X-ray powder diffraction data. Several model structures were derived from the structure of the selenium rich phase CuInSe{sub 2.3} by permuting the cations in the available Wyckoff positions. The refinement of the best model by the Rietveld method in the tetragonal space group P anti 42c (N 112), Z=1, with unit cell parameters a=5.7762(2) Aa, c=11.5982(7) Aa and V=386.97(3) Aa{sup 3} led to R{sub p}=8.0%, R{sub wp}=9.6%, R{sub exp}=6.2% and {chi}{sup 2}=1.7 for 134 independent reflections. The model that best fitted the diffraction data has the following atomic distribution: Cu in Wyckoff site 2f; Fe in Wyckoff site 2d; In in Wyckoff site 2b and 1/3Cu, 1/3Fe, 1/3In in Wyckoff site 2f; Se in Wyckoff site 8n. (copyright 2007 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  10. Insights into the mechanism of X-ray-induced disulfide-bond cleavage in lysozyme crystals based on EPR, optical absorption and X-ray diffraction studies.

    Science.gov (United States)

    Sutton, Kristin A; Black, Paul J; Mercer, Kermit R; Garman, Elspeth F; Owen, Robin L; Snell, Edward H; Bernhard, William A

    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. 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.

  11. 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.

  12. The Incorporation of Single Crystal X-Ray Diffraction into the Undergraduate Chemistry Curriculum Using Internet-Facilitated Remote Diffractometer Control

    Science.gov (United States)

    Szalay, P. S.; Hunter, A. D.; Zeller, M.

    2005-01-01

    The benefits of integrating single crystal X-ray diffraction into the curricula of the disciplines of science such as chemistry, biology, biochemistry physics, and many more are addressed. The results showed that students were able to complete all report requirements with the aid of handouts and instructor inputs, and remote control of the…

  13. The Incorporation of Single Crystal X-Ray Diffraction into the Undergraduate Chemistry Curriculum Using Internet-Facilitated Remote Diffractometer Control

    Science.gov (United States)

    Szalay, P. S.; Hunter, A. D.; Zeller, M.

    2005-01-01

    The benefits of integrating single crystal X-ray diffraction into the curricula of the disciplines of science such as chemistry, biology, biochemistry physics, and many more are addressed. The results showed that students were able to complete all report requirements with the aid of handouts and instructor inputs, and remote control of the…

  14. 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

  15. Single-crystal X-ray diffraction and NMR crystallography of a 1:1 cocrystal of dithianon and pyrimethanil.

    Science.gov (United States)

    Pöppler, Ann Christin; Corlett, Emily K; Pearce, Harriet; Seymour, Mark P; Reid, Matthew; Montgomery, Mark G; Brown, Steven P

    2017-03-01

    A single-crystal X-ray diffraction structure of a 1:1 cocrystal of two fungicides, namely dithianon (DI) and pyrimethanil (PM), is reported [systematic name: 5,10-dioxo-5H,10H-naphtho[2,3-b][1,4]dithiine-2,3-dicarbonitrile-4,6-dimethyl-N-phenylpyrimidin-2-amine (1/1), C14H4N2O2S2·C12H13N2]. Following an NMR crystallography approach, experimental solid-state magic angle spinning (MAS) NMR spectra are presented together with GIPAW (gauge-including projector augmented wave) calculations of NMR chemical shieldings. Specifically, experimental (1)H and (13)C chemical shifts are determined from two-dimensional (1)H-(13)C MAS NMR correlation spectra recorded with short and longer contact times so as to probe one-bond C-H connectivities and longer-range C...H proximities, whereas H...H proximities are identified in a (1)H double-quantum (DQ) MAS NMR spectrum. The performing of separate GIPAW calculations for the full periodic crystal structure and for isolated molecules allows the determination of the change in chemical shift upon going from an isolated molecule to the full crystal structure. For the (1)H NMR chemical shifts, changes of 3.6 and 2.0 ppm correspond to intermolecular N-H...O and C-H...O hydrogen bonding, while changes of -2.7 and -1.5 ppm are due to ring current effects associated with C-H...π interactions. Even though there is a close intermolecular S...O distance of 3.10 Å, it is of note that the molecule-to-crystal chemical shifts for the involved sulfur or oxygen nuclei are small.

  16. Room-temperature serial crystallography using a kinetically optimized microfluidic device for protein crystallization and on-chip X-ray diffraction

    Directory of Open Access Journals (Sweden)

    Michael Heymann

    2014-09-01

    Full Text Available An emulsion-based serial crystallographic technology has been developed, in which nanolitre-sized droplets of protein solution are encapsulated in oil and stabilized by surfactant. Once the first crystal in a drop is nucleated, the small volume generates a negative feedback mechanism that lowers the supersaturation. This mechanism is exploited to produce one crystal per drop. Diffraction data are measured, one crystal at a time, from a series of room-temperature crystals stored on an X-ray semi-transparent microfluidic chip, and a 93% complete data set is obtained by merging single diffraction frames taken from different unoriented crystals. As proof of concept, the structure of glucose isomerase was solved to 2.1 Å, demonstrating the feasibility of high-throughput serial X-ray crystallography using synchrotron radiation.

  17. Preparation, crystallization, and preliminary X-ray diffraction study of mutant carboxypeptidase T containing the primary specificity pocket of carboxypeptidase B

    Energy Technology Data Exchange (ETDEWEB)

    Akparov, V. Kh., E-mail: valery@akparov.ru; Grishin, A. M. [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. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2010-09-15

    Recombinant G215S, A251G, T257A, D260G, T262D mutant carboxypeptidase T from Thermoactinomyces vulgaris containing mutations in the primary specificity pocket was prepared and crystallized. Single crystals with a size of up to 0.3 mm were grown and investigated by X-ray diffraction. Recombinant mutant carboxypeptidase T containing the primary specificity subsite compositionally identical to that of pancreatic carboxypeptidase B crystallizes in the same space group as the natural enzyme. The crystals belong to sp. gr. P6{sub 3}22; the unit-cell parameters are a = b = 157.867 A, c = 104.304 A, {alpha} = {beta} = 90 deg., {gamma} = 120 deg. X-ray diffraction data suitable for determining the three-dimensional structure at atomic resolution were collected from one crystal.

  18. The Crystal Structure of Thorium and Zirconium Dihydrides by X-ray and Neutron Diffraction

    Science.gov (United States)

    Rundle, R.E.; Shull, C.G.; Wollan, E.O.

    1951-04-20

    Thorium forms a tetragonal lower hydride of composition ThH{sub 2}. The hydrides ThH{sub 2}, ThD{sub 2}, and ZrD{sub 2} have been studied by neutron diffraction in order that hydrogen positions could be determined. The hydrides are isomorphous, and have a deformed fluorite structure. Metal-hydrogen distances in thorium hydride are unusually large, as in UH{sub 3}. Thorium and zirconium scattering amplitudes and a revised scattering amplitude for deuterium are reported.

  19. 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.

  20. Characterization of Metalloproteins and Biomaterials by X-ray Absorption Spectroscopy and X-ray Diffraction

    DEFF Research Database (Denmark)

    Frankær, Christian Grundahl

    This thesis presents thework on combining complementary X-rays techniques for studying the structures of proteins and other biomaterials, and consists of three different projects: (i) Characterization of protein powders with X-ray powder diffraction (XRPD). (ii) The combination of X......-ray crystallography and X-ray absorption spectroscopy (XAS) applied to studying different hexameric insulin conformations. (iii) The structures of polymorphs of strontium ranelate and the distribution of strontium in bone tissue. A procedure for fast identification and verification of protein powders using XRPD...... was developed and tested on micro-crystals of lysozyme and insulin. Different protein crystal forms were identified by comparing experimental powder diffraction patternswith patterns calculated from PDB coordinates. The key factor to bring the calculated patterns in agreement with the observed patterns...

  1. Crystallization and preliminary X-ray diffraction results of snowdrop (Galanthus nivalis) lectin.

    Science.gov (United States)

    Wright, C S; Kaku, H; Goldstein, I J

    1990-01-25

    Well-ordered single crystals have been grown for a mannose-specific lectin from snowdrop (Galanthus nivalis) bulbs in the presence of methyl-alpha-D-mannoside. The space group symmetry is consistent with the orthorhombic space group P2(1)2(1)2(1). The unit cell parameters are a = 140.0 A, b = 64.7 A, c = 62.0 A. The asymmetric unit can accommodate a tetramer. The functional molecule (50,000 daltons) consists of four identical subunits and is highly specific for alpha 1,3-linked mannose oligosaccharides.

  2. The Crystal Structure of the Malaria Pigment Hemozoin as Elucidated by X-ray Powder Diffraction

    DEFF Research Database (Denmark)

    Straasø, Tine

    in the eradication of malaria. This thesis is a step towards that goal. When examining red blood cells from an infected person under a microscope dark pigment is observed. This dark pigment is actually small crystals called hemozoin. Hemozoin is a by-product formed by the parasite and a necessity for parasitic....... As part of the project an all-in-vacuum powder diffractometer was developed, which provides data with a minimum background level and an improved signal-to-noise ratio. Moreover, the diffractometer is designed with the particular purpose of decreasing the number of parameters to be fitted. Installation...... of the diffractometer at the 60 keV beamline at PETRA III, resulted in data from a diamond powder to unpreceded resolution providing accurate structure factors suitable for advanced electron density modelling....

  3. X-ray Powder Diffraction in Conservation Science: Towards Routine Crystal Structure Determination of Corrosion Products on Heritage Art Objects.

    Science.gov (United States)

    Dinnebier, Robert E; Fischer, Andrea; Eggert, Gerhard; Runčevski, Tomče; Wahlberg, Nanna

    2016-06-08

    The crystal structure determination and refinement process of corrosion products on historic art objects using laboratory high-resolution X-ray powder diffraction (XRPD) is presented in detail via two case studies. The first material under investigation was sodium copper formate hydroxide oxide hydrate, Cu4Na4O(HCOO)8(OH)2∙4H2O (sample 1) which forms on soda glass/copper alloy composite historic objects (e.g., enamels) in museum collections, exposed to formaldehyde and formic acid emitted from wooden storage cabinets, adhesives, etc. This degradation phenomenon has recently been characterized as "glass induced metal corrosion". For the second case study, thecotrichite, Ca3(CH3COO)3Cl(NO3)2∙6H2O (sample 2), was chosen, which is an efflorescent salt forming needlelike crystallites on tiles and limestone objects which are stored in wooden cabinets and display cases. In this case, the wood acts as source for acetic acid which reacts with soluble chloride and nitrate salts from the artifact or its environment. The knowledge of the geometrical structure helps conservation science to better understand production and decay reactions and to allow for full quantitative analysis in the frequent case of mixtures.

  4. Single-crystal X-ray diffraction study of Fe2SiO4 fayalite up to 31 GPa

    Science.gov (United States)

    Zhang, Jin S.; Hu, Yi; Shelton, Hannah; Kung, Jennifer; Dera, Przemyslaw

    2016-10-01

    Olivine is widely believed to be the most abundant mineral in the Earth's upper mantle. Here, we report structural refinement results for the Fe-end-member olivine, Fe2SiO4 fayalite, up to 31 GPa in diamond-anvil cell, using single-crystal synchrotron X-ray diffraction. Unit-cell parameters a, b, c and V, average Si-O Fe-O bond lengths, as well as Si-O Fe-O polyhedral volumes continuously decrease with increasing pressure. The pressure derivative of isothermal bulk modulus K_{T0}^' } is determined to be 4.0 (2) using third-order Birch-Murnaghan equation of state with ambient isothermal bulk modulus fixed to 135 GPa on the basis of previous Brillouin measurements. The Si-O tetrahedron is stiffer than the Fe-O octahedra, and the compression mechanism is dominated by Fe-O bond and Fe-O octahedral compression. Densities of olivine along 1600 and 900 K adiabats are calculated based on this study. The existence of metastable olivine inside the cold subduction slab could cause large positive buoyancy force against subduction, slow down the subduction and possibly affect the slab geometry.

  5. Crystal structures of crotonaldehyde semicarbazone and crotonaldehyde thiosemicarbazone from X-ray powder diffraction data

    Directory of Open Access Journals (Sweden)

    Atef Arfan

    2015-02-01

    Full Text Available Crotonaldehyde semicarbazone {systematic name: (E-2-[(E-but-2-en-1-ylidene]hydrazinecarboxamide}, C5H9N3O, (I, and crotonaldehyde thiosemicarbazone {systematic name: (E-2-[(E-but-2-en-1-yldene]hydrazinecarbothioamide}, C5H9N3S, (II, show the same E conformation around the imine C=N bond. Compounds (I and (II were obtained by the condensation of crotonaldehyde with semicarbazide hydrochloride and thiosemicarbazide, respectively. Each molecule has an intramolecular N—H...N hydrogen bond, which generates an S(5 ring. In (I, the crotonaldehyde fragment is twisted by 2.59 (5° from the semicarbazide mean plane, while in (II the corresponding angle (with the thiosemicarbazide mean plane is 9.12 (5°. The crystal packing is different in the two compounds: in (I intermolecular N—H...O hydrogen bonds link the molecules into layers parallel to the bc plane, while weak intermolecular N—H...S hydrogen bonds in (II link the molecules into chains propagating in [110].

  6. Crystallization and preliminary X-ray diffraction studies of θ-toxin (perfringolysin O), a pore-forming cytolysin of Clostridium perfringens

    Science.gov (United States)

    Sugahara, Mitsuaki; Sekino-Suzuki, Naoko; Ohno-Iwashita, Yoshiko; Miki, Kunio

    1996-10-01

    θ-Toxin (perfringolysin O), a cholesterol-binding, pore-forming cytolysin of Clostridium perfringens type A was crystallized by the vapor diffusion procedure using polyethyleneglycol 4000 and sodium chloride as precipitants in 2-(cyclohexylamino)ethanesulfonic acid (CHES) buffer at pH 9.5. The diffraction patterns of precession photographs indicated that the crystals belong to the orthorhombic system and the space group C222 1 with unit-cell dimensions of a = 47.7 Å, b = 182.0 Å and c = 175.8 Å. Assuming that the asymmetric unit contains one or two molecules (Mw 52 700), the Vm value is calculated as 3.6 or 1.8 Å 3/dalton, respectively. The crystals diffract X-rays to at least 3 Å resolution and are suitable for high resolution X-ray crystal structure determination.

  7. Structural characterization of Li1.2v3o8 insertion electrodes by single-crystal x-ray-diffraction

    CSIR Research Space (South Africa)

    De

    1993-08-01

    Full Text Available The crystal structures of Li1.2V3O8 and a lithiated product Li4.0V3O8 have been determined by single-crystal X-ray diffraction methods. The structure refinement of Li1.2V308 confirms that of Li1+xV3O8(x almost-equal-to 0) reported by Wadsley thirty...

  8. 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.

  9. Observation of strong virtual scattering under three-beam (220, 371) X-ray diffraction in TeO{sub 2} single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Blagov, A. E.; Kovalchuk, M. V. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation); Kohn, V. G. [Kurchatov Institute, Russian Research Centre (Russian Federation); Pisarevskii, Yu. V.; Prosekov, P. A., E-mail: aopt@ns.crys.ras.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2010-01-15

    A strong effect of virtual scattering has been experimentally observed when studying the nearly coplanar three-beam (220, 371) X-ray diffraction in a paratellurite single crystal under high-resolution double-crystal X-ray diffraction using MoK{sub {alpha}1} radiation. One characteristic feature of this effect is that the angular dependence of the first (strong) reflection intensity and its shape barely change in the three-beam range of parameters, whereas very strong changes are observed for the second (weak) reflection not only in the three-beam range but also far beyond it, which is related to the variation in the two-beam diffraction parameter due to virtual scattering. The changes observed are asymmetric and make it possible to determine the triplet combination of structure-factor phases.

  10. Possibilities and limitations of synchrotron X-ray powder diffraction with double crystal and double multilayer monochromators for microscopic speciation studies

    Energy Technology Data Exchange (ETDEWEB)

    De Nolf, Wout [Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610, Antwerpen (Wilrijk) (Belgium)], E-mail: wout.denolf@ua.ac.be; Jaroszewicz, Jakub [Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610, Antwerpen (Wilrijk) (Belgium); Terzano, Roberto [Dipartimento di Biologia e Chimica Agro-forestale ed Ambientale, Via Amendola 165/A, I-70126, University of Bari, Bari (Italy); Lind, Ole Christian; Salbu, Brit [Isotope Laboratory, Norwegian University of Life Sciences, PO Box 5003, N-1432 As (Norway); Vekemans, Bart [Department of Analytical Chemistry, Ghent University, Krijgslaan 281 S12, B-9000 Gent (Belgium); Janssens, Koen [Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610, Antwerpen (Wilrijk) (Belgium); Falkenberg, Gerald [HASYLAB at DESY, Beamline L, Notkestraat 85, D-22603, Hamburg (Germany)

    2009-08-15

    The performance of a combined microbeam X-ray fluorescence/X-ray powder diffraction (XRF/XRPD) measurement station at Hamburger Synchrotronstrahlungslabor (HASYLAB) Beamline L is discussed in comparison to that at European Synchrotron Radiation Facility (ESRF) ID18F/ID22. The angular resolution in the X-ray diffractograms is documented when different combinations of X-ray source, optics and X-ray diffraction detectors are employed. Typical angular resolution values in the range 0.3-0.5 deg. are obtained at the bending magnet source when a 'pink' beam form of excitation is employed. A similar setup at European Synchrotron Radiation Facility beamlines ID18F and ID22 allows to reach angular resolution values of 0.1-0.15 deg. In order to document the possibilities and limitations for speciation of metals in environmental materials by means of Hamburger Synchrotronstrahlungslabor Beamline L X-ray fluorescence/X-ray powder diffraction setup, two case studies are discussed, one involved in the identification of the crystal phases in which heavy metals such as chromium, iron, barium and lead are present in polluted soils of an industrial site (Val Basento, Italy) and another involved in the speciation of uranium in depleted uranium particles (Ceja Mountains, Kosovo). In the former case, the angular resolution is sufficient to allow identification of most crystalline phases present while in the latter case, it is necessary to dispose of an angular resolution of ca. 0.2 deg. to distinguish between different forms of oxidized uranium.

  11. Limit of hydrostaticity in He and Ne determined by means of in situ single crystal x-ray diffraction

    Science.gov (United States)

    Kurnosov, Alexander; Trots, Dmitro; Boffa Balaran, Tiziana; Frost, Daniel

    2010-05-01

    An ultrahigh-intensity rotating anode FR-E+ SuperBright from Rigaku coupled with a Huber four circle diffractometer and VariMaxTM focusing optics has been used to determine accurate and precise lattice parameters of very small single-crystals in diamond anvil cells at pressures above 40 GPa in a conventional laboratory. The optics are focusing the X-ray beam at the sample position (800 mm from the aperture of the optics) to the spot of about 200 μm size with high resolution (as measured by the sharp reflections line widths). The intensities of reflections from any crystal are at least 30 times larger than those obtained for the same sample with a similar x-ray diffractometer equipped with a conventional x-ray tube. However, accurate and precise lattice parameters at high pressure can be obtained only under hydrostatic or at least very close to hydrostatic conditions in order to avoid broadening of the reflections. To test the quasi-hydrostatic limits of He and Ne we have therefore performed a study of single crystals of quartz up to amorphisation of the sample and MgO single crystals. The study of these materials has also the advantage of being able to obtain compare the pressure scale of these two very well known materials with that of the ruby scale which appears to be dependent on the pressure medium used.

  12. 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.

  13. Structures of an asymmetrically coupled double-well superlattice by double-crystal X-ray diffraction

    Institute of Scientific and Technical Information of China (English)

    马文全; 庄岩; 王玉田; 江德生

    1997-01-01

    An asymmetrically coupled ( GaAs/AlAs/GaAs/AlAs)/GaAs(001) double-well supperlattice isstudied by HRDCD (high resolution double-crystal X-ray diffractometry).The intensity of satellite peaks is modulated by wave packet of different sublayers.In the course of simulation,the satellite peaks in the vicinity of the node points of wave packet are very informative for precise determination of sublayer thickness and for improving accuracy.

  14. Synchrotron-based crystal structure, associated morphology of snail and bivalve shells by X-ray diffraction

    Science.gov (United States)

    Rao, D. V.; Gigante, G. E.; Kumar, Y. Manoj; Cesareo, R.; Brunetti, A.; Schiavon, N.; Akatsuka, T.; Yuasa, T.; Takeda, T.

    2016-10-01

    Synchrotron-based high-resolution X-ray powder diffraction spectra from the body parts of a snail and bivalve (CaCO3), have been recorded with Pilatus area detector. Experiments were performed at Desy, Hamburg, Germany, utilizing the Resonant and Diffraction beamline (P9), with 15 keV X-rays (λ=0.82666 Å). The external shell of these living organisms, is composed of calcium carbonate, which carries strong biological signal. It consists of some light elements, such as, Ca, C and O, which constitute part of the soft tissue and other trace elements. The knowledge of these diffraction patterns and hence the understanding of structures at molecular level are enormous. The application of synchrotron radiation to powder diffraction is well suited for samples of biological nature via changes in their patterns and also to investigate crystallographic phase composition. With the use of Rietveld refinement procedure, to the high-resolution diffraction spectra, we were able to extract the lattice parameters of orthorhombic polymorph of CaCO3, the most abundant mineral produced by these living organisms. The small size of the crystallite is a very important factor related to the biological structure. The natural model presents a combination of organic and inorganic phases with nanometer size. For the present study, we also used the scanning electron microscopy (SEM) to explore the associated morphology of the snail and bivalve.

  15. Crystallization and preliminary X-ray diffraction study of phosphopantetheine adenylyltransferase from M. tuberculosis crystallizing in space group P3{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Timofeev, V. I., E-mail: tostars@mail.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation); Chupova, L. A.; 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)

    2015-09-15

    Crystals of M. tuberculosis phosphopantetheine adenylyltransferase 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 2.00-Å resolution. The crystals belong to sp. gr. P3{sub 2} and have the following unit-cell parameters: a = b = 106.47 Å, c = 71.32 Å, α = γ = 90°, β = 120°. The structure was solved by the molecular-replacement method. There are six subunits of the enzyme comprising a hexamer per asymmetric unit. The hexamer is a biologically active form of phosphopantetheine adenylyltransferase from M. tuberculosis.

  16. 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.

  17. Single Particle X-ray Diffractive Imaging

    Energy Technology Data Exchange (ETDEWEB)

    Bogan, M J; Benner, W H; Boutet, S; Rohner, U; Frank, M; Seibert, M; Maia, F; Barty, A; Bajt, S; Riot, V; Woods, B; Marchesini, S; Hau-Riege, S P; Svenda, M; Marklund, E; Spiller, E; Hajdu, J; Chapman, H N

    2007-10-01

    In nanotechnology, strategies for the creation and manipulation of nanoparticles in the gas phase are critically important for surface modification and substrate-free characterization. Recent coherent diffractive imaging with intense femtosecond X-ray pulses has verified the capability of single-shot imaging of nanoscale objects at sub-optical resolutions beyond the radiation-induced damage threshold. By intercepting electrospray-generated particles with a single 15 femtosecond soft-X-ray pulse, we demonstrate diffractive imaging of a nanoscale specimen in free flight for the first time, an important step toward imaging uncrystallized biomolecules.

  18. Coherent X-ray diffraction studies of mesoscopic materials

    Energy Technology Data Exchange (ETDEWEB)

    Shabalin, Anatoly

    2015-12-15

    This thesis is devoted to three separate projects, which can be considered as independent. First, the dynamical scattering effects in the Coherent X-ray Diffractive Imaging (CXDI) method are discussed. Based on the simulation results, a straightforward method for correction for the refraction and absorption artifacts in the Bragg CXDI reconstruction is suggested. The second part summarizes the results of an Coherent X-ray Diffractive Imaging experiment with a single colloidal crystal grain. A remarkable result is that positions of individual particles in the crystal lattice have been resolved in three dimensions. The third project is devoted to X-ray diffraction experimental studies of structural evolution of colloidal crystalline films upon incremental heating. Based on the results of the analysis a model of structural evolution of a colloidal crystal upon heating on nanoscopic and mesoscopic length scales is suggested.

  19. 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.

  20. Crystal structure of dicesium hydrogen citrate from laboratory single-crystal and powder X-ray diffraction data and DFT comparison.

    Science.gov (United States)

    Rammohan, Alagappa; Sarjeant, Amy A; Kaduk, James A

    2017-02-01

    The crystal structure of dicesium hydrogen citrate, 2Cs(+)·C6H6O7(2-), has been solved using laboratory X-ray single-crystal diffraction data, refined using laboratory powder X-ray data, and optimized using density functional techniques. The Cs(+) cation is nine-coordinate, with a bond-valence sum of 0.92 valence units. The CsO9 coordination polyhedra share edges and corners to form a three-dimensional framework. The citrate anion is located on a mirror plane. Its central hy-droxy/carboxyl-ate O-H⋯O hydrogen bond is short, and (unusually) inter-molecular. The centrosymmetric end-end carboxyl-ate hydrogen bond is exceptionally short (O⋯O = 2.416 Å) and strong. These hydrogen bonds contribute 16.5 and 21.7 kcal mol(-1), respectively, to the crystal energy. The hydro-phobic methyl-ene groups occupy pockets in the framework.

  1. Crystal structure of dicesium hydrogen citrate from laboratory single-crystal and powder X-ray diffraction data and DFT comparison

    Science.gov (United States)

    Rammohan, Alagappa; Sarjeant, Amy A.; Kaduk, James A.

    2017-01-01

    The crystal structure of dicesium hydrogen citrate, 2Cs+·C6H6O7 2−, has been solved using laboratory X-ray single-crystal diffraction data, refined using laboratory powder X-ray data, and optimized using density functional techniques. The Cs+ cation is nine-coordinate, with a bond-valence sum of 0.92 valence units. The CsO9 coordination polyhedra share edges and corners to form a three-dimensional framework. The citrate anion is located on a mirror plane. Its central hy­droxy/carboxyl­ate O—H⋯O hydrogen bond is short, and (unusually) inter­molecular. The centrosymmetric end-end carboxyl­ate hydrogen bond is exceptionally short (O⋯O = 2.416 Å) and strong. These hydrogen bonds contribute 16.5 and 21.7 kcal mol−1, respectively, to the crystal energy. The hydro­phobic methyl­ene groups occupy pockets in the framework. PMID:28217349

  2. Crystal structures of cristobalite-type and coesite-type PON redetermined on the basis of single-crystal X-ray diffraction data

    Directory of Open Access Journals (Sweden)

    Maxim Bykov

    2015-11-01

    Full Text Available Hitherto, phosphorus oxonitride (PON could not be obtained in the form of single crystals and only powder diffraction experiments were feasible for structure studies. In the present work we have synthesized two polymorphs of phosphorus oxonitride, cristobalite-type (cri-PON and coesite-type (coe-PON, in the form of single crystals and reinvestigated their crystal structures by means of in house and synchrotron single-crystal X-ray diffraction. The crystal structures of cri-PON and coe-PON are built from PO2N2 tetrahedral units, each with a statistical distribution of oxygen and nitrogen atoms. The crystal structure of the coe-PON phase has the space group C2/c with seven atomic sites in the asymmetric unit [two P and three (N,O sites on general positions, one (N,O site on an inversion centre and one (N,O site on a twofold rotation axis], while the cri-PON phase possesses tetragonal I-42d symmetry with two independent atoms in the asymmetric unit [the P atom on a fourfold inversion axis and the (N,O site on a twofold rotation axis]. In comparison with previous structure determinations from powder data, all atoms were refined with anisotropic displacement parameters, leading to higher precision in terms of bond lengths and angles.

  3. Crystal structures of cristobalite-type and coesite-type PON redetermined on the basis of single-crystal X-ray diffraction data.

    Science.gov (United States)

    Bykov, Maxim; Bykova, Elena; Dyadkin, Vadim; Baumann, Dominik; Schnick, Wolfgang; Dubrovinsky, Leonid; Dubrovinskaia, Natalia

    2015-11-01

    Hitherto, phospho-rus oxonitride (PON) could not be obtained in the form of single crystals and only powder diffraction experiments were feasible for structure studies. In the present work we have synthesized two polymorphs of phospho-rus oxonitride, cristobalite-type (cri-PON) and coesite-type (coe-PON), in the form of single crystals and reinvestigated their crystal structures by means of in house and synchrotron single-crystal X-ray diffraction. The crystal structures of cri-PON and coe-PON are built from PO2N2 tetra-hedral units, each with a statistical distribution of oxygen and nitro-gen atoms. The crystal structure of the coe-PON phase has the space group C2/c with seven atomic sites in the asymmetric unit [two P and three (N,O) sites on general positions, one (N,O) site on an inversion centre and one (N,O) site on a twofold rotation axis], while the cri-PON phase possesses tetra-gonal I-42d symmetry with two independent atoms in the asymmetric unit [the P atom on a fourfold inversion axis and the (N,O) site on a twofold rotation axis]. In comparison with previous structure determinations from powder data, all atoms were refined with anisotropic displacement parameters, leading to higher precision in terms of bond lengths and angles.

  4. Crystallization, Preliminary X-ray Diffraction and Structure Solution of MosA, a Dihydrodipicolinate Synthase from Sinorhizobium Meliloti L5-30

    Energy Technology Data Exchange (ETDEWEB)

    Leduc,Y.; Phenix, C.; Puttick, J.; Nienaber, K.; Palmer, D.; Delbaere, L.

    2006-01-01

    The structure of MosA, a dihydrodipicolinate synthase and reported methyltransferase from Sinorhizobium meliloti, has been solved using molecular replacement with Escherichia coli dihydrodipicolinate synthase as the model. A crystal grown in the presence of pyruvate diffracted X-rays to 2.3 Angstroms resolution using synchrotron radiation and belonged to the orthorhombic space group C2221, with unit-cell parameters a = 69.14, b = 138.87, c = 124.13 Angstroms.

  5. Photoluminescence and X-ray Diffraction of Distributed Bragg Reflector

    Institute of Scientific and Technical Information of China (English)

    LI Lin; LI Yong-da; LIU Wen-li; LU Bin; JU Guo-xian; ZHANG Yong-ming; HAO Yong-qin; SU Wei; ZHONG Jing-chang

    2004-01-01

    Spectral and structural characteristics of distributed Bragg reflector (DBR) in vertical-cavity surface-emitting lasers were studied with photoluminescence and double- crystal X- ray diffraction measurement. The expected high quality epitaxial DBR structure was verified. In the X- ray double- crystal rocking curves of DBR the zeroth- order peak, the first and second order satellite peaks were measured.Splitting of diffraction peak appeared in the rocking curves was analyzed. The effects of introduced deep energy levels on the structural perfection and optical properties were discussed.

  6. Low-temperature phase transition in glycine-glutaric acid co-crystals studied by single-crystal X-ray diffraction, Raman spectroscopy and differential scanning calorimetry.

    Science.gov (United States)

    Zakharov, Boris A; Losev, Evgeniy A; Kolesov, Boris A; Drebushchak, Valeri A; Boldyreva, Elena V

    2012-06-01

    The occurrence of a first-order reversible phase transition in glycine-glutaric acid co-crystals at 220-230 K has been confirmed by three different techniques - single-crystal X-ray diffraction, polarized Raman spectroscopy and differential scanning calorimetry. The most interesting feature of this phase transition is that every second glutaric acid molecule changes its conformation, and this fact results in the space-group symmetry change from P2(1)/c to P1. The topology of the hydrogen-bonded motifs remains almost the same and hydrogen bonds do not switch to other atoms, although the hydrogen bond lengths do change and some of the bonds become inequivalent.

  7. Aligned hemozoin crystals in curved clusters in malarial red blood cells revealed by nanoprobe X-ray Fe fluorescence and diffraction

    DEFF Research Database (Denmark)

    Kapishnikov, Sergey; Berthing, Trine; Hviid, Lars

    2012-01-01

    The human malaria parasite Plasmodium falciparum detoxifies the heme byproduct of hemoglobin digestion in infected red blood cells by sequestration into submicron-sized hemozoin crystals. The crystal is composed of heme units interlinked to form cyclic dimers via reciprocal Fe-O (propionate) bonds...... fluorescence and diffraction. The X-ray patterns indicated the presence of hemozoin clusters, each comprising several crystals aligned along their needle c axes and exposing {100} side faces to an approximately cylindrical surface, suggestive of nucleation via a common lipid layer. This experimental finding...

  8. The determination of crystal structures of active pharmaceutical ingredients from X-ray powder diffraction data: a brief, practical introduction, with fexofenadine hydrochloride as example.

    Science.gov (United States)

    Brüning, Jürgen; Schmidt, Martin U

    2015-06-01

    This study describes the general method for the determination of the crystal structures of active pharmaceutical ingredients (API) from powder diffraction data and demonstrates its use to determine the hitherto unknown crystal structure of fexofenadine hydrochloride, a third-generation antihistamine drug. Fexofenadine hydrochloride was subjected to a series of crystallisation experiments using re-crystallisation from solvents, gas diffusion, layering with an antisolvent and gel crystallisation. Powder diffraction patterns of all samples were recorded and inspected for polymorphism and for crystallinity. All samples corresponded to the same polymorph. The crystal structure was determined from an X-ray powder diffraction pattern using a real-space method with subsequent Rietveld refinement. The structure exhibits a two-dimensional hydrogen bond network. Crystal structures of API can be determined from X-ray powder diffraction data with good reliability. Fexofenadine exhibits only one polymorphic form, which is stabilised in the crystal by strong hydrogen bonds of the type (+)N-H···Cl(-), O-H···Cl(-), and between COOH groups. © 2015 Royal Pharmaceutical Society.

  9. 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.

  10. Solvent exchange in a metal-organic framework single crystal monitored by dynamic in situ X-ray diffraction.

    Science.gov (United States)

    Cox, Jordan M; Walton, Ian M; Bateman, Gage; Benson, Cassidy A; Mitchell, Travis; Sylvester, Eric; Chen, Yu Sheng; Benedict, Jason B

    2017-08-01

    Understanding the processes by which porous solid-state materials adsorb and release guest molecules would represent a significant step towards developing rational design principles for functional porous materials. To elucidate the process of liquid exchange in these materials, dynamic in situ X-ray diffraction techniques have been developed which utilize liquid-phase chemical stimuli. Using these time-resolved diffraction techniques, the ethanol solvation process in a flexible metal-organic framework [Co(AIP)(bpy)0.5(H2O)]·2H2O was examined. The measurements provide important insight into the nature of the chemical transformation in this system including the presence of a previously unreported neat ethanol solvate structure.

  11. A Novel Method for Studying Thermal Motion and Point Defects in Crystals by X-Ray Resonant Diffraction

    Science.gov (United States)

    Dmitrienko, V. E.; Ishida, K.; Kirfel, A.; Kokubun, J.; Ovchinnikova, E. N.

    2003-01-01

    After an introductory survey of the X-ray resonant anisotropy, we present a novel X-ray method to observe thermal-motion-induced (TMI) and point-defect-induced (PDI) distortions of electronic states of atoms. This method uses the idea that, in general, the local atomic environment becomes less symmetric owing to point defects and/or the thermal vibrations of the atoms in a crystal. As a result of this phenomenon, an additional anisotropy of the resonant scattering factors can occur and "forbidden" Bragg reflections can be excited near the absorption edges. Examples of crystals are discussed (Ge, Y3Fe5O12) where TMI and PDI reflections can be found. The tensor structure factors of the both types of reflections are calculated. According to our theory, the TMI reflection structure factors are proportional to the vibration correlations, u∥2 and u⊥2, of neighboring atoms, and it is inferred that u∥2 provides the main contribution to the thermal-motion-induced anisotropy of X-ray resonant scattering. The TMI reflections in Ge were recently observed by Kokubun et al. (Phys. Rev. B64, 073203 (2001)), Kirfel et al. (in press), and Colella et al. (in press) in accordance with our prediction. For the 006 reflection, the intensity increases about 25 times with the temperature increasing from 30 to 735 K. Owing to their resonant character, the PDI reflections allow to separately study both impurity atoms and host atoms of different types. The considered phenomena can provide a very sensitive method for studying point defects because only the atoms that are affected by defects contribute to the PDI reflections.

  12. 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.

  13. Diffraction leveraged modulation of X-ray pulses using MEMS-based X-ray optics

    Science.gov (United States)

    Lopez, Daniel; Shenoy, Gopal; Wang, Jin; Walko, Donald A.; Jung, Il-Woong; Mukhopadhyay, Deepkishore

    2016-08-09

    A method and apparatus are provided for implementing Bragg-diffraction leveraged modulation of X-ray pulses using MicroElectroMechanical systems (MEMS) based diffractive optics. An oscillating crystalline MEMS device generates a controllable time-window for diffraction of the incident X-ray radiation. The Bragg-diffraction leveraged modulation of X-ray pulses includes isolating a particular pulse, spatially separating individual pulses, and spreading a single pulse from an X-ray pulse-train.

  14. High-pressure phase diagram and equation of state of solid helium from single-crystal X-ray diffraction to 23.3 GPa

    Science.gov (United States)

    Mao, H. K.; Hemley, R. J.; Jephcoat, A. P.; Finger, L. W.; Wu, Y.

    1988-01-01

    Single-crystal X-ray diffraction measurements have been performed on solid He-4 from 15.6 to 23.3 GPa at 300 K with synchrotron radiation. The diffraction patterns demonstrate that the structure of the solid is hexagonal close packed over this pressure-temperature range, contrary to both the interpretation of high-pressure optical studies and to theoretical predictions. The solid is more compressible than is indicated by equations of state calculated with recently determined helium pair potentials. The results suggest that a significant revision of current views of the phase diagram and energetics of dense solid helium is in order.

  15. 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.

  16. Disorder in the composite crystal structure of the manganese `disilicide' MnSi1.73 from powder X-ray diffraction data.

    Science.gov (United States)

    Akselrud, L; Cardoso Gil, R; Wagner-Reetz, M; Grin, Yu

    2015-12-01

    The crystal structure of the higher manganese silicide MnSi1.7 (known in the literature as HMS) is investigated in samples with different compositions obtained by different techniques at temperatures not higher than 1273 K. Powder X-ray diffraction was applied. The crystal structure is described as incommensurate composite. In addition to the ordered model already known in the literature, the partial disorder in the silicon substructure was detected and described introducing an additional atomic site with a different modulation function.

  17. Synthesis and X-ray Powder Diffraction Characterization of A New Niobate Crystal Ba4Na2VNb9O30

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    A new niobate crystal Ba4Na2VNb9O30 was synthesized in BaO-Na2O-V2O5-Nb2O5 system for the first time.Its shape,optical properties,melting point and chemical stability were studied.X-ray powder diffraction study determined that this compound assumes a tetragonal tungsten bronze structure with space group P4bm(100) and lattice parameters a=b=12.4275(2),c=3.970(3).The new compound may be one kind of photorefractive crystals.

  18. 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.

  19. 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.

  20. Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex.

    Science.gov (United States)

    Lyubimov, Artem Y; Uervirojnangkoorn, Monarin; Zeldin, Oliver B; Zhou, Qiangjun; Zhao, Minglei; Brewster, Aaron S; Michels-Clark, Tara; Holton, James M; Sauter, Nicholas K; Weis, William I; Brunger, Axel T

    2016-10-12

    X-ray free electron lasers (XFELs) reduce the effects of radiation damage on macromolecular diffraction data and thereby extend the limiting resolution. Previously, we adapted classical post-refinement techniques to XFEL diffraction data to produce accurate diffraction data sets from a limited number of diffraction images (Uervirojnangkoorn et al., 2015), and went on to use these techniques to obtain a complete data set from crystals of the synaptotagmin-1 / SNARE complex and to determine the structure at 3.5 Å resolution (Zhou et al., 2015). Here, we describe new advances in our methods and present a reprocessed XFEL data set of the synaptotagmin-1 / SNARE complex. The reprocessing produced small improvements in electron density maps and the refined atomic model. The maps also contained more information than those of a lower resolution (4.1 Å) synchrotron data set. Processing a set of simulated XFEL diffraction images revealed that our methods yield accurate data and atomic models.

  1. A Practical Method of Simulating X-Ray Diffraction

    Science.gov (United States)

    Brisse, F.; Sundararajan, P. R.

    1975-01-01

    Describes an experiment in which the beam of X-rays is simulated through the use of a laser as a monochromatic light source and the crystal is replaced by photographically prepared masks. A strong diffraction pattern as large as 20 cm. can be obtained. (GS)

  2. A Practical Method of Simulating X-Ray Diffraction

    Science.gov (United States)

    Brisse, F.; Sundararajan, P. R.

    1975-01-01

    Describes an experiment in which the beam of X-rays is simulated through the use of a laser as a monochromatic light source and the crystal is replaced by photographically prepared masks. A strong diffraction pattern as large as 20 cm. can be obtained. (GS)

  3. Crystal structures of the trifluoromethyl sulfonates M(SO3CF3)2 (M = Mg, Ca, Ba, Zn, Cu) from synchrotron X-ray powder diffraction data.

    Science.gov (United States)

    Dinnebier, Robert; Sofina, Natalia; Hildebrandt, Lars; Jansen, Martin

    2006-06-01

    The crystal structures of divalent metal salts of trifluoromethyl sulfonic acid ("trifluoromethyl sulfonates") M(SO(3)CF(3))(2) (M = Mg, Ca, Ba, Zn, Cu) were determined from high-resolution X-ray powder diffraction data. Magnesium, calcium and zinc trifluoromethyl sulfonate crystallize in the rhombohedral space group R(bar)3. Barium trifluoromethyl sulfonate crystallizes in the monoclinic space group I2/a(C2/c) and copper trifluoromethyl sulfonate crystallizes in the triclinic group P(bar)1. Within the crystal structures the trifluoromethyl sulfonate anions are arranged in double layers with the apolar CF(3) groups pointing towards each other. The cations are located next to the SO(3) groups. The symmetry relations between the different crystal structures have been analysed.

  4. Crystal Structures of the Trifluoromethyl Sulfonates M(SO3CF3)2 (M = Mg, Ca, Ba, Zn, Cu) from Synchrotron X-ray Powder Diffraction Data

    Energy Technology Data Exchange (ETDEWEB)

    Dinnebier,R.; Sofina, N.; Hildebrandt, L.; Jansen, M.

    2006-01-01

    The crystal structures of divalent metal salts of trifluoromethyl sulfonic acid ('trifluoromethyl sulfonates') M(SO{sub 3}CF{sub 3}){sub 2} (M = Mg, Ca, Ba, Zn, Cu) were determined from high-resolution X-ray powder diffraction data. Magnesium, calcium and zinc trifluoromethyl sulfonate crystallize in the rhombohedral space group R{bar 3}. Barium trifluoromethyl sulfonate crystallizes in the monoclinic space group I2/a(C2/c) and copper trifluoromethyl sulfonate crystallizes in the triclinic group P{bar 1}. Within the crystal structures the trifluoromethyl sulfonate anions are arranged in double layers with the apolar CF{sub 3} groups pointing towards each other. The cations are located next to the SO{sub 3} groups. The symmetry relations between the different crystal structures have been analyzed.

  5. Purification, crystallization and preliminary X-ray diffraction of the G3BP1 NTF2-like domain

    DEFF Research Database (Denmark)

    Vognsen, Tina; Möller, Ingvar Rúnar; Kristensen, Ole

    2011-01-01

    The nuclear transport factor 2-like (NTF2-like) domain of human G3BP1 was subcloned, overexpressed in Escherichia coli and purified. Crystals were obtained using the hanging-drop vapour-diffusion method. Diffraction data were collected to 3.6 Å resolution using synchrotron radiation. The crystals...

  6. 5-Arylidene derivatives of Meldrum's acid: Synthesis, structural characterization using single crystal and powder crystal X-ray diffraction, and electronic properties

    Science.gov (United States)

    Dey, Tanusri; Ghosh, Soumen; Ghosh, Somnath; Mukherjee, Alok Kumar

    2015-07-01

    Four 5-arylidene derivatives of Meldrum's acid, 5-(4-chlorobenzylidene)-2,2-dimethyl-1,3-dioxane-4,6-dione (2), 5-(3-hydroxybenzylidene)-2,2-dimethyl-1,3-dioxane-4,6-dione (3), 5-(3,4-dimethoxybenzylidene)-2,2-dimethyl-1,3-dioxane-4,6-dione (4) and 5-(2,4-dimethoxy benzylidene)-2,2-dimethyl-1,3-dioxane-4,6-dione (5) have been synthesized and their crystal structures have been determined using single crystal X-ray diffractometry for 2, 4 and 5 and X-ray powder diffraction for 3. The nature of intermolecular interactions in 2-5 has been analyzed through Hirshfeld surfaces and 2D fingerprint plots. The DFT optimized molecular geometries in 2-5 agree closely with those obtained from the crystallographic studies. The crystal packing in 2-5 exhibits an interplay of Osbnd H⋯O, Csbnd H⋯O, Csbnd H⋯Cl and Csbnd H⋯π (arene) hydrogen bonds and π⋯π interactions, which assemble molecules into three-dimensional architecture in 2, 3 and 5 and two-dimensional framework in 4. The Hirshfeld surface analyses of 2-5, Meldrum's acid (1) and a few related 5-arylidene derivatives of Meldrum's acid retrieved from the Cambridge Structural Database (CSD) indicate that about 85% of the Hirshfeld surface area (72% in 2 where H⋯Cl contribution is about 13%) in this class of compounds are due to H⋯H, O⋯H and C⋯H contacts. The HOMO-LUMO energy gap (>2.2 eV) in 2-5 indicates a significant degree of internal charge transfer within the molecule.

  7. 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.

  8. Optical properties of X-rays--dynamical diffraction.

    Science.gov (United States)

    Authier, André

    2012-01-01

    The first attempts at measuring the optical properties of X-rays such as refraction, reflection and diffraction are described. The main ideas forming the basis of Ewald's thesis in 1912 are then summarized. The first extension of Ewald's thesis to the X-ray case is the introduction of the reciprocal lattice. In the next step, the principles of the three versions of the dynamical theory of diffraction, by Darwin, Ewald and Laue, are given. It is shown how the comparison of the dynamical and geometrical theories of diffraction led Darwin to propose his extinction theory. The main optical properties of X-ray wavefields at the Bragg incidence are then reviewed: Pendellösung, shift of the Bragg peak, fine structure of Kossel lines, standing waves, anomalous absorption, paths of wavefields inside the crystal, Borrmann fan and double refraction. Lastly, some of the modern applications of the dynamical theory are briefly outlined: X-ray topography, location of adsorbed atoms at crystal surfaces, optical devices for synchrotron radiation and X-ray interferometry.

  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. Bulk Crystal Growth, and High-Resolution X-ray Diffraction Results of LiZnAs Semiconductor Material

    Science.gov (United States)

    Montag, Benjamin W.; Reichenberger, Michael A.; Sunder, Madhana; Ugorowski, Philip B.; Nelson, Kyle A.; Henson, Luke C.; McGregor, Douglas S.

    2017-08-01

    LiZnAs is being explored as a candidate for solid-state neutron detectors. The compact form, solid-state device would have greater efficiency than present day gas-filled 3He and 10BF3 detectors. Devices fabricated from LiZnAs having either natural Li (nominally 7.5% 6Li) or enriched 6Li (usually 95% 6Li) as constituent atoms may provide a material for compact high efficiency neutron detectors. The 6Li( n, t)4He reaction yields a total Q-value of 4.78 MeV, an energy larger than that of the 10B reaction, which can easily be identified above background radiations. LiZnAs material was synthesized by preparing equimolar portions of Li, Zn, and As sealed under vacuum (10-6 Torr) in quartz ampoules lined with boron nitride and subsequently reacted in a compounding furnace (Montag et al. in J Cryst Growth 412:103, 2015). The raw synthesized LiZnAs was purified by a static vacuum sublimation in quartz (Montag et al. in J Cryst Growth 438:99, 2016). Bulk crystalline LiZnAs ingots were grown from the purified material with a high-temperature Bridgman-style growth process described here. One of the largest LiZnAs ingots harvested was 9.6 mm in diameter and 4.2 mm in length. Samples were harvested from the ingot and were characterized for crystallinity using a Bruker AXS Inc. D8 AXS Inc. D2 CRYSO, energy dispersive x-ray diffractometer, and a Bruker AXS Inc. D8 DISCOVER, high-resolution x-ray diffractometer equipped with molybdenum radiation, Gobel mirror, four bounce germanium monochromator and a scintillation detector. The primary beam divergence was determined to be 0.004°, using a single crystal Si standard. The x-ray based characterization revealed that the samples nucleated in the (110) direction and a high-resolution open detector rocking curve recorded on the (220) LiZnAs yielded a full width at half maximum (FWHM) of 0.235°. Sectional pole figures using off-axis reflections of the (211) LiZnAs confirmed in-plane ordering, and also indicated the presence of multiple

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. Crystallization and preliminary X-ray diffraction analyses of the TIR domains of three TIR-NB-LRR proteins that are involved in disease resistance in Arabidopsis thaliana.

    Science.gov (United States)

    Wan, Li; Zhang, Xiaoxiao; Williams, Simon J; Ve, Thomas; Bernoux, Maud; Sohn, Kee Hoon; Jones, Jonathan D G; Dodds, Peter N; Kobe, Bostjan

    2013-11-01

    The Toll/interleukin-1 receptor (TIR) domain is a protein-protein interaction domain that is found in both animal and plant immune receptors. The N-terminal TIR domain from the nucleotide-binding (NB)-leucine-rich repeat (LRR) class of plant disease-resistance (R) proteins has been shown to play an important role in defence signalling. Recently, the crystal structure of the TIR domain from flax R protein L6 was determined and this structure, combined with functional studies, demonstrated that TIR-domain homodimerization is a requirement for function of the R protein L6. To advance the molecular understanding of the function of TIR domains in R-protein signalling, the protein expression, purification, crystallization and X-ray diffraction analyses of the TIR domains of the Arabidopsis thaliana R proteins RPS4 (resistance to Pseudomonas syringae 4) and RRS1 (resistance to Ralstonia solanacearum 1) and the resistance-like protein SNC1 (suppressor of npr1-1, constitutive 1) are reported here. RPS4 and RRS1 function cooperatively as a dual resistance-protein system that prevents infection by three distinct pathogens. SNC1 is implicated in resistance pathways in Arabidopsis and is believed to be involved in transcriptional regulation through its interaction with the transcriptional corepressor TPR1 (Topless-related 1). The TIR domains of all three proteins have successfully been expressed and purified as soluble proteins in Escherichia coli. Plate-like crystals of the RPS4 TIR domain were obtained using PEG 3350 as a precipitant; they diffracted X-rays to 2.05 Å resolution, had the symmetry of space group P1 and analysis of the Matthews coefficient suggested that there were four molecules per asymmetric unit. Tetragonal crystals of the RRS1 TIR domain were obtained using ammonium sulfate as a precipitant; they diffracted X-rays to 1.75 Å resolution, had the symmetry of space group P4(1)2(1)2 or P4(3)2(1)2 and were most likely to contain one molecule per asymmetric

  18. Utilizing broadband X-rays in a Bragg coherent X-ray diffraction imaging experiment

    Energy Technology Data Exchange (ETDEWEB)

    Cha, Wonsuk; Liu, Wenjun; Harder, Ross; Xu, Ruqing; Fuoss, Paul H.; Hruszkewycz, Stephan O.

    2016-07-26

    A method is presented to simplify Bragg coherent X-ray diffraction imaging studies of complex heterogeneous crystalline materials with a two-stage screening/imaging process that utilizes polychromatic and monochromatic coherent X-rays and is compatible within situsample environments. Coherent white-beam diffraction is used to identify an individual crystal particle or grain that displays desired properties within a larger population. A three-dimensional reciprocal-space map suitable for diffraction imaging is then measured for the Bragg peak of interest using a monochromatic beam energy scan that requires no sample motion, thus simplifyingin situchamber design. This approach was demonstrated with Au nanoparticles and will enable, for example, individual grains in a polycrystalline material of specific orientation to be selected, then imaged in three dimensions while under load.

  19. Utilizing broadband X-rays in a Bragg coherent X-ray diffraction imaging experiment.

    Science.gov (United States)

    Cha, Wonsuk; Liu, Wenjun; Harder, Ross; Xu, Ruqing; Fuoss, Paul H; Hruszkewycz, Stephan O

    2016-09-01

    A method is presented to simplify Bragg coherent X-ray diffraction imaging studies of complex heterogeneous crystalline materials with a two-stage screening/imaging process that utilizes polychromatic and monochromatic coherent X-rays and is compatible with in situ sample environments. Coherent white-beam diffraction is used to identify an individual crystal particle or grain that displays desired properties within a larger population. A three-dimensional reciprocal-space map suitable for diffraction imaging is then measured for the Bragg peak of interest using a monochromatic beam energy scan that requires no sample motion, thus simplifying in situ chamber design. This approach was demonstrated with Au nanoparticles and will enable, for example, individual grains in a polycrystalline material of specific orientation to be selected, then imaged in three dimensions while under load.

  20. Crystallization and preliminary X-ray diffraction studies of maleylacetate reductase from Rhizobium sp. strain MTP-10005

    Energy Technology Data Exchange (ETDEWEB)

    Fujii, Tomomi; Goda, Yuko [Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011 (Japan); Yoshida, Masahiro; Oikawa, Tadao [Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, Suita, Osaka 564-8680 (Japan); Hata, Yasuo, E-mail: hata@scl.kyoto-u.ac.jp [Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011 (Japan)

    2008-08-01

    Maleylacetate reductase from Rhizobium sp. strain MTP-10005 has been crystallized using the sitting-drop vapour-diffusion method and microseeding. The crystals contained one dimeric molecule per asymmetric unit and diffracted to 1.79 Å resolution. Maleylacetate reductase (EC 1.3.1.32), which catalyzes the reduction of maleylacetate to 3-oxoadipate, plays an important role in the aerobic microbial catabolism of resorcinol. The enzyme has been crystallized at 293 K by the sitting-drop vapour-diffusion method supplemented with a microseeding technique, using ammonium sulfate as the precipitating agent. The crystal belonged to the monoclinic space group C2, with unit-cell parameters a = 56.85, b = 121.13, c = 94.09 Å, β = 101.48°, and contained one dimeric molecule in the asymmetric unit. It diffracted to 1.79 Å resolution.

  1. The behavior of single-crystal silicon to dynamic loading using in-situ X-ray diffraction and phase contrast imaging

    Science.gov (United States)

    Lee, Hae Ja; Xing, Zhou; Galtier, Eric; Arnold, Brice; Granados, Eduardo; Brown, Shaughnessy B.; Tavella, Franz; McBride, Emma; Fry, Alan; Nagler, Bob; Schropp, Andreas; Seiboth, Frank; Samberg, Dirk; Schroer, Christian; Gleason, Arianna E.; Higginbotham, Andrew

    Hydrostatic and uniaxial compression studies have revealed that crystalline silicon undergoes phase transitions from a cubic diamond structure to a variety of phases including orthorhombic Imma phase, body-centered tetragonal phase, and a hexagonal primitive phase. The dynamic response of silicon at high pressure, however, is not well understood. Phase contrast imaging has proven to be a powerful tool for probing density changes caused by the shock propagation into a material. In order to characterize the elastic and phase transitions, we image shock waves in Si with high spatial resolution using the LCLS X-ray free electron laser and Matter in Extreme Conditions instrument. In this study, the long pulse optical laser with pseudo-flat top shape creates high pressures up to 60 GPa. We measure the crystal structure by observing X-ray diffraction orthogonal to the shock propagation direction over a range of pressures. We describe the capability of simultaneously performing phase contrast imaging and in situ X-ray diffraction during shock loading and discuss the dynamic response of Si in high-pressure phases Use of the Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract No. DE-AC02-76SF00515. The MEC instrument is supported by.

  2. Crystallization and preliminary X-ray diffraction studies of polyketide synthase-1 (PKS-1) from Cannabis sativa

    Energy Technology Data Exchange (ETDEWEB)

    Taguchi, Chiho [Faculty of Pharmaceutical Sciences, Kyushu University (Japan); Quantum Beam Science Directorate, Japan Atomic Energy Agency (Japan); Taura, Futoshi [Faculty of Pharmaceutical Sciences, Kyushu University (Japan); Tamada, Taro; Shoyama, Yoshinari [Quantum Beam Science Directorate, Japan Atomic Energy Agency (Japan); Shoyama, Yukihiro; Tanaka, Hiroyuki [Faculty of Pharmaceutical Sciences, Kyushu University (Japan); Kuroki, Ryota, E-mail: kuroki.ryota@jaea.go.jp [Quantum Beam Science Directorate, Japan Atomic Energy Agency (Japan); Morimoto, Satoshi [Faculty of Pharmaceutical Sciences, Kyushu University (Japan)

    2008-03-01

    Polyketide synthase-1 from C. sativa has been crystallized. The crystal diffracted to 1.55 Å resolution with sufficient quality for further structure determination. Polyketide synthase-1 (PKS-1) is a novel type III polyketide synthase that catalyzes the biosynthesis of hexanoyl triacetic acid lactone in Cannabis sativa (Mexican strain). PKS-1 was overproduced in Escherichia coli, purified and finally crystallized in two different space groups. The crystal obtained in 0.1 M HEPES buffer pH 7.5 containing 0.2 M calcium acetate and 20%(w/v) polyethylene glycol 3350 diffracted to 1.65 Å resolution and belonged to space group P1, with unit-cell parameters a = 54.3, b = 59.3, c = 62.6 Å, α = 69, β = 81, γ = 80°. Another crystal obtained in 0.1 M HEPES buffer pH 7.5 containing 0.2 M sodium chloride and 20%(w/v) polyethylene glycol 3350 diffracted to 1.55 Å resolution and belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 54.3, b = 110, c = 130 Å. These data will enable us to determine the crystal structure of PKS-1.

  3. 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.

  4. X-ray diffraction contrast tomography (DCT) system, and an X-ray diffraction contrast tomography (DCT) method

    DEFF Research Database (Denmark)

    2012-01-01

    Source: US2012008736A An X-ray diffraction contrast tomography system (DCT) comprising a laboratory X-ray source (2), a staging device (5) rotating a polycrystalline material sample in the direct path of the X-ray beam, a first X-ray detector (6) detecting the direct X-ray beam being transmitted...... through the crystalline material sample, a second X-ray detector (7) positioned between the staging device and the first X-ray detector for detecting diffracted X-ray beams, and a processing device (15) for analysing detected values. The crystallographic grain orientation of the individual grain...

  5. Use of X-ray diffraction, molecular simulations, and spectroscopy to determine the molecular packing in a polymer-fullerene bimolecular crystal

    Energy Technology Data Exchange (ETDEWEB)

    Miller, Nichole Cates; Gysel, Roman; Sweetnam, Sean; McGehee, Michael D. [Department of Materials Science and Engineering, Stanford University, Stanford, CA (United States); Cho, Eunkyung [School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA (United States); School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA (United States); Junk, Matthias J.N.; Chmelka, Bradley F. [Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA (United States); Risko, Chad; Kim, Dongwook; Bredas, Jean-Luc [School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA (United States); Miller, Chad E. [Department of Materials Science and Engineering, Stanford University, Stanford, CA (United States); Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA (United States); Richter, Lee J.; Kline, R. Joseph [National Institute of Standards and Technology, Gaithersburg, MD (United States); Heeney, Martin; McCulloch, Iain [Department of Chemistry, Imperial College London (United Kingdom); Amassian, Aram [King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Thuwal (Saudi Arabia); Acevedo-Feliz, Daniel; Knox, Christopher [King Abdullah University of Science and Technology (KAUST), Visualization Core Laboratory, Thuwal (Saudi Arabia); Hansen, Michael Ryan; Dudenko, Dmytro [Max Planck Institute for Polymer Research, Mainz (Germany); Toney, Michael F. [Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA (United States)

    2012-11-27

    The molecular packing in a polymer: fullerene bimolecular crystal is determined using X-ray diffraction (XRD), molecular mechanics (MM) and molecular dynamics (MD) simulations, 2D solid-state NMR spectroscopy, and IR absorption spectroscopy. The conformation of the electron-donating polymer is significantly disrupted by the incorporation of the electron-accepting fullerene molecules, which introduce twists and bends along the polymer backbone and 1D electron-conducting fullerene channels. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  6. Organobase catalyzed 1,4-conjugate addition of 4-hydroxycoumarin on chalcones: Synthesis, NMR and single-crystal X-ray diffraction studies of novel warfarin analogues

    Science.gov (United States)

    Talhi, Oualid; Fernandes, José A.; Pinto, Diana C. G. A.; Almeida Paz, Filipe A.; Silva, Artur M. S.

    2015-08-01

    The synthesis of a new series of warfarin analogues by convenient organobase catalyzed 1,4-conjugate addition of 4-hydroxycoumarin to chalcone derivatives is described. 1H NMR spectroscopy evidenced the presence of a predominant acyclic open-form together with the cyclic hemiketal tautomers of the resulting Michael adducts. The acyclic open-form has been unequivocally proved by single-crystal X-ray diffraction analysis. The use of the B ring ortho-hydroxychalcone synthons in this reaction has led to a diastereoselective synthesis of warfarin bicyclo[3.3.1]nonane ketal derivatives.

  7. Use of X-ray diffraction, molecular simulations, and spectroscopy to determine the molecular packing in a polymer-fullerene bimolecular crystal

    KAUST Repository

    Miller, Nichole Cates

    2012-09-05

    The molecular packing in a polymer: fullerene bimolecular crystal is determined using X-ray diffraction (XRD), molecular mechanics (MM) and molecular dynamics (MD) simulations, 2D solid-state NMR spectroscopy, and IR absorption spectroscopy. The conformation of the electron-donating polymer is significantly disrupted by the incorporation of the electron-accepting fullerene molecules, which introduce twists and bends along the polymer backbone and 1D electron-conducting fullerene channels. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. 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.

  9. High pressure x-ray diffraction techniques with synchrotron radiation

    Institute of Scientific and Technical Information of China (English)

    刘景

    2016-01-01

    This article summarizes the developments of experimental techniques for high pressure x-ray diffraction (XRD) in diamond anvil cells (DACs) using synchrotron radiation. Basic principles and experimental methods for various diffraction geometry are described, including powder diffraction, single crystal diffraction, radial diffraction, as well as coupling with laser heating system. Resolution in d-spacing of different diffraction modes is discussed. More recent progress, such as extended application of single crystal diffraction for measurements of multigrain and electron density distribution, time-resolved diffraction with dynamic DAC and development of modulated heating techniques are briefl y introduced. The current status of the high pressure beamline at BSRF (Beijing Synchrotron Radiation Facility) and some results are also presented.

  10. 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)

  11. Expression, Crystallization and Preliminary X-ray Diffraction Analyses of Med-ORF10 in the Biosynthetic Pathway of an Antitumor Antibiotic Medermycin.

    Science.gov (United States)

    Liu, Yanli; Liu, Shasha; Yang, Tingting; Guo, Xiaoxia; Jiang, Yali; Zahid, Kashif Rafiq; Liu, Ke; Liu, Jinlin; Yang, Jihong; Zhao, Haobin; Yang, Yi; Li, Aiying; Qi, Chao

    2015-12-01

    Medermycin, as a prominent member of benzoisochromanequinones, possesses strong antitumor activity and is biosynthesized under the control of a 29-ORF-containing biosynthetic gene cluster. Most of ORFs in this gene cluster have not been characterized, including a small protein encoding gene med-ORF10, proposed to play a regulatory role in biosynthesis of medermycin in an unknown mode. In this study, we reported the expression, protein preparation, crystallization and preliminary X-ray diffraction analyses of Med-ORF10 of the wild type Streptomyces strain. Firstly, we cloned and overexpressed med-ORF10 in Escherichia coli and purified the protein with 98% purity and 3 mg/L yield. Then, we crystallized the protein at concentration of 20 mg/mL in condition 22% PEG 3350, 0.2 M magnesium formate and collected the data at 1.78 Å resolution. Finally, we detected the expression of Med-ORF10 in Streptomyces by western blotting. In conclusion, this study confirmed the expression of Med-ORF10 protein in the wild-type strain of Streptomyces AM-7161 and collected the X-ray diffraction data of Med-ORF10 crystal at 1.78 Å resolution. These studies provide evidences for the functional Med-ORF10 protein in Streptomyces strains and facilitate our further investigation.

  12. 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

  13. 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.

  14. Superlattice structure of Ce{sup 3+}-doped BaMgF{sub 4} fluoride crystals - x-ray diffraction, electron spin-resonance, and optical investigations

    Energy Technology Data Exchange (ETDEWEB)

    Yamaga, M.; Hattori, K. [Department of Electrical and Electronic Engineering, Faculty of Engineering, Gifu University, Gifu (Japan); Kodama, N. [Department of Materials Science and Engineering, Faculty of Engineering and Resource Science, Akita University, Akita (Japan); Ishizawa, N. [Materials and Structures Laboratory, Tokyo Institute of Technology, Yokohama (Japan); Honda, M. [Faculty of Science, Naruto University of Education, Naruto (Japan); Shimamura, K.; Fukuda, T. [Institute for Materials Research, Tohoku University, Sendai (Japan)

    2001-09-14

    The x-ray diffraction patterns for Ce{sup 3+}-doped BaMgF{sub 4} (BMF) crystals suggest the existence of superlattice structure. The superlattice model is consistent with the characterization of the 4f{sup 1} ground state of Ce{sup 3+} as a probe ion using the electron spin-resonance (ESR) technique. The distinct Ce{sup 3+} luminescence spectra with different peak energies and lifetimes also support the superlattice model. Although the detailed superlattice structure could not be analysed using the diffraction spots, a model has been proposed, taking into account the eight Ce{sup 3+} polyhedra with different anion coordinations in the unit cell of the BMF crystal obtained from the ESR experiments. (author)

  15. Incoherent Diffractive Imaging via Intensity Correlations of Hard X Rays

    Science.gov (United States)

    Classen, Anton; Ayyer, Kartik; Chapman, Henry N.; Röhlsberger, Ralf; von Zanthier, Joachim

    2017-08-01

    Established x-ray diffraction methods allow for high-resolution structure determination of crystals, crystallized protein structures, or even single molecules. While these techniques rely on coherent scattering, incoherent processes like fluorescence emission—often the predominant scattering mechanism—are generally considered detrimental for imaging applications. Here, we show that intensity correlations of incoherently scattered x-ray radiation can be used to image the full 3D arrangement of the scattering atoms with significantly higher resolution compared to conventional coherent diffraction imaging and crystallography, including additional three-dimensional information in Fourier space for a single sample orientation. We present a number of properties of incoherent diffractive imaging that are conceptually superior to those of coherent methods.

  16. 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

  17. A posteriori design of crystal contacts to improve the X-ray diffraction properties of a small RNA enzyme

    Energy Technology Data Exchange (ETDEWEB)

    MacElrevey, Celeste [Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642 (United States); Spitale, Robert C. [Department of Chemistry, Biological Chemistry Cluster, River Campus Box 270216, University of Rochester, Rochester, New York 14627-0216 (United States); Krucinska, Jolanta [Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642 (United States); Wedekind, Joseph E., E-mail: joseph.wedekind@rochester.edu [Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642 (United States); Department of Chemistry, Biological Chemistry Cluster, River Campus Box 270216, University of Rochester, Rochester, New York 14627-0216 (United States)

    2007-07-01

    Insertion of a dangling 5′-uracil and incorporation of synthetic linkers at the domain interface of a minimal hairpin ribozyme have been investigated as means of favorably influencing crystal packing. These modifications lead to changes in the ribozyme’s structural elements that mimic packing within a natural four-way helical junction, thereby providing an example of how knowledge-based design can be used to enhance the diffraction properties of a tertiarily folded RNA. The hairpin ribozyme is a small catalytic RNA comprising two helix–loop–helix domains linked by a four-way helical junction (4WJ). In its most basic form, each domain can be formed independently and reconstituted without a 4WJ to yield an active enzyme. The production of such minimal junctionless hairpin ribozymes is achievable by chemical synthesis, which has allowed structures to be determined for numerous nucleotide variants. However, abasic and other destabilizing core modifications hinder crystallization. This investigation describes the use of a dangling 5′-U to form an intermolecular U·U mismatch, as well as the use of synthetic linkers to tether the loop A and B domains, including (i) a three-carbon propyl linker (C3L) and (ii) a nine-atom triethylene glycol linker (S9L). Both linker constructs demonstrated similar enzymatic activity, but S9L constructs yielded crystals that diffracted to 2.65 Å resolution or better. In contrast, C3L variants diffracted to 3.35 Å and exhibited a 15 Å expansion of the c axis. Crystal packing of the C3L construct showed a paucity of 6{sub 1} contacts, which comprise numerous backbone to 2′-OH hydrogen bonds in junctionless and S9L complexes. Significantly, the crystal packing in minimal structures mimics stabilizing features observed in the 4WJ hairpin ribozyme structure. The results demonstrate how knowledge-based design can be used to improve diffraction and overcome otherwise destabilizing defects.

  18. 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.

  19. 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

  20. Crystallization and preliminary X-ray diffraction studies of NP24-I, an isoform of a thaumatin-like protein from ripe tomato fruits

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, Raka; Chakrabarti, Chandana, E-mail: chandana.chakrabarti@saha.ac.in [Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata 700064 (India)

    2005-08-01

    A thaumatin-like antifungal protein, NP24-I, has been isolated from ripe tomato fruits. It was crystallized by the vapour-diffusion method and data were collected to 2.45 Å. The structure was solved by molecular replacement. NP24 is a 24 kDa (207-amino-acid) antifungal thaumatin-like protein (TLP) found in tomato fruits. An isoform of the protein, NP24-I, is reported to play a possible role in ripening of the fruit in addition to its antifungal properties. The protein has been isolated and purified and crystallized by the hanging-drop vapour-diffusion method. The crystals belong to the tetragonal space group P4{sub 3}, with unit-cell parameters a = b = 61.01, c = 62.90 Å and one molecule per asymmetric unit. X-ray diffraction data were processed to a resolution of 2.45 Å and the structure was solved by molecular replacement.

  1. In situ Raman and synchrotron X-ray diffraction study on crystallization of Choline chloride/Urea deep eutectic solvent under high pressure

    Science.gov (United States)

    Yuan, Chaosheng; Chu, Kunkun; Li, Haining; Su, Lei; Yang, Kun; Wang, Yongqiang; Li, Xiaodong

    2016-09-01

    Pressure-induced crystallization of Choline chloride/Urea (ChCl/Urea) deep eutectic solvent (DES) has been investigated by in-situ Raman spectroscopy and synchrotron X-ray diffraction. The results indicated that high pressure crystals appeared at around 2.6 GPa, and the crystalline structure was different from that formed at ambient pressure. Upon increasing the pressure, the Nsbnd H stretching modes of Urea underwent dramatic change after liquid-solid transition. It appears that high pressures may enhance the hydrogen bonds formed between ChCl and Urea. P versus T phase diagram of ChCl/Urea DES was constructed, and the crystallization mechanism of ChCl/Urea DES was discussed in view of hydrogen bonds.

  2. 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.

  3. 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....

  4. Observation of pressure-induced phase transition of δ-AlOOH by using single-crystal synchrotron X-ray diffraction method

    Science.gov (United States)

    Kuribayashi, Takahiro; Sano-Furukawa, Asami; Nagase, Toshiro

    2014-04-01

    Pressure-induced phase transition of δ-AlOOH was confirmed between 6.1 and 8.2 GPa by using a single-crystal synchrotron X-ray diffraction method. The phase transition is reversible and unquenchable. Results from analysis of the distribution of X-ray diffraction intensities at 8.2 GPa reveal an additional systematic, absence of k + l odd for 0 kl in comparison with h + l odd for h0 l observed prior to the phase transition (space group, P21 nm). The space group of the post-transition phase should be Pnnm or Pnn2 to satisfy the systematic absence rule. Crystal structure refinements of the post-transition phase conducted for the three models ( Pnnm, Pnn2, and P21 nm) indicate that the space group of the post-transition phase is Pnnm. The O-O distance of hydrogen bond in the post-transition phase at 8.2 GPa is 2.439(6) Å and is significantly longer than the predicted distance (2.366 Å) of the hydrogen bond symmetrization in δ-AlOOH. The H distribution in the post-transition phase would display a fully disordered hydrogen bond pattern.

  5. Purification, crystallization and preliminary X-ray diffraction studies to near-atomic resolution of dihydrodipicolinate synthase from methicillin-resistant Staphylococcus aureus

    Energy Technology Data Exchange (ETDEWEB)

    Burgess, Benjamin R.; Dobson, Renwick C. J., E-mail: rdobson@unimelb.edu.au; Dogovski, Con [Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010 (Australia); Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, Parkville, Victoria 3010 (Australia); Jameson, Geoffrey B. [Centre for Structural Biology, Institute of Fundamental Sciences, Massey University, Palmerston North (New Zealand); 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, Parkville, Victoria 3010 (Australia); St Vincents Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065 (Australia); Perugini, Matthew A., E-mail: rdobson@unimelb.edu.au [Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010 (Australia); Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, Parkville, Victoria 3010 (Australia)

    2008-07-01

    Dihydrodipicolinate synthase (DHDPS), an enzyme of the lysine-biosynthetic pathway, is a promising target for antibiotic development against pathogenic bacteria. Here, the expression, purification, crystallization and preliminary diffraction analysis to 1.45 Å resolution of DHDPS from methicillin-resistant S. aureus is reported. In recent years, dihydrodipicolinate synthase (DHDPS; EC 4.2.1.52) has received considerable attention from both mechanistic and structural viewpoints. DHDPS is part of the diaminopimelate pathway leading to lysine, coupling (S)-aspartate-β-semialdehyde with pyruvate via a Schiff base to a conserved active-site lysine. In this paper, the cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of DHDPS from methicillin-resistant Staphylococcus aureus, an important bacterial pathogen, are reported. The enzyme was crystallized in a number of forms, predominantly from PEG precipitants, with the best crystal diffracting to beyond 1.45 Å resolution. The space group was P1 and the unit-cell parameters were a = 65.4, b = 67.6, c = 78.0 Å, α = 90.1, β = 68.9, γ = 72.3°. The crystal volume per protein weight (V{sub M}) was 2.34 Å{sup 3} Da{sup −1}, with an estimated solvent content of 47% for four monomers per asymmetric unit. The structure of the enzyme will help to guide the design of novel therapeutics against the methicillin-resistant S. aureus pathogen.

  6. Crystallization and preliminary X-ray diffraction studies of the cysteine protease ervatamin A from Ervatamia coronaria

    Energy Technology Data Exchange (ETDEWEB)

    Chakraborty, Sibani; Biswas, Sampa; Chakrabarti, Chandana; Dattagupta, Jiban K., E-mail: jibank.dattagupta@saha.ac.in [Saha Institue of Nuclear Physics, Crystallography and Molecular Biology Division, 1/AF Bidhannagar, Kolkata 700 064 (India)

    2005-06-01

    Ervatamin A is a papain-family cysteine protease with high activity and stability. It has been isolated and purified from the latex of the medicinal flowering plant E. coronaria and crystallized by the vapour-diffusion technique. Crystals diffracted to 2.1 Å and the structure was solved by molecular replacement. The ervatamins are highly stable cysteine proteases that are present in the latex of the medicinal plant Ervatamia coronaria and belong to the papain family, members of which share similar amino-acid sequences and also a similar fold comprising two domains. Ervatamin A from this family, a highly active protease compared with others from the same source, has been purified to homogeneity by ion-exchange chromatography and crystallized by the vapour-diffusion method. Needle-shaped crystals of ervatamin A diffract to 2.1 Å resolution and belong to space group C222{sub 1}, with unit-cell parameters a = 31.10, b = 144.17, c = 108.61 Å. The solvent content using an ervatamin A molecular weight of 27.6 kDa is 43.9%, with a V{sub M} value of 2.19 Å{sup 3} Da{sup −1} assuming one protein molecule in the asymmetric unit. A molecular-replacement solution has been found using the structure of ervatamin C as a search model.

  7. 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.

  8. 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.

  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. X-ray diffraction comparator - new possibilities.

    Science.gov (United States)

    Brytov, I A; Dmitriev, G D; Ivanov, V N; Klevtsov, S A

    1997-01-01

    We have studied the possibilities to determine precisely the lattice constants of quartz using an X-ray diffractometer-comparator. This device has double-crystal optical scheme, continuously swinging crystal-monochromator and an original angular reference system. The measurement strategy uses the difference in angular positions of two different Bragg planes relative the third one. On assumption that the wavelength of the used radiation is known with accuracy of ± 1.2,ppm, the accuracy of determined lattice constants is estimated in ± 5×10-5Å. The described measurement strategy proves to be efficient in measuring the changes of the lattice constants with temperature and in precision testing of a quartz single-crystal homogeneity. We discuss also the features of other instruments for the automatic sorting of quartz blanks in groups by the cut angle, which use the same monochromator pendulum system.

  12. Ultrafast Time Resolved X-ray Diffraction Studies of Laser Heated Metals and Semiconductors

    Science.gov (United States)

    Chen, Peilin; Tomov, I. V.; Rentzepis, P. M.

    1998-03-01

    Time resolved hard x-ray diffraction has been employed to study the dynamics of lattice structure deformation. When laser pulse energy is deposited in a material it generates a non uniform transient temperature distribution, which alters the lattice structure of the crystal. The deformed crystal lattice will change the angle of diffraction for a monochromatic x-ray beam. We report picosecond and nanosecond time resolved x-ray diffraction measurements of the lattice temperature distribution, transient structure and stress, in Pt (111) and GaAs (111) crystals, caused by pulsed UV laser irradiation. An ArF excimer laser operated at 300 Hz was used, both, to drive an x-ray diode with copper anode and heat the crystal. Bragg diffracted x-ray radiation was recorded by a direct imaging x-ray CCD. Changes in the diffraction patterns induced by a few millijouls pulse energy were observed at different time delays between the laser heating pulse and the x-ray probing pulse. A kinematical model for time resolved x-ray diffraction was used to analyze the experimental data. Good agreement between the measured and calculated scattered x-ray intensities profiles was achieved, indicating that detailed time resolved x-ray diffraction measurements can be made with nanosecond and picosecond resolution for small temperature changes. Our system can detect changes in the lattice spacing of about 10-3 A.

  13. In-situ X-ray diffraction studies of time and thickness dependence of crystallization of amorphous TiO{sub 2} thin films and stress evolution

    Energy Technology Data Exchange (ETDEWEB)

    Kuzel, R., E-mail: kuzel@karlov.mff.cuni.c [Department of Condensed Matter Physics, Faculty of Mathematics and Physics, Charles University in Prague, 121 16 Praha 2 (Czech Republic); Nichtova, L.; Matej, Z. [Department of Condensed Matter Physics, Faculty of Mathematics and Physics, Charles University in Prague, 121 16 Praha 2 (Czech Republic); Musil, J. [Department of Physics, Faculty of Applied Sciences, University of West Bohemia in Pilsen, Pilsen (Czech Republic)

    2010-12-30

    Remarkable properties of titanium dioxide films such as hydrophilicity or photocatalytic activity depend largely on their phase composition, microstructure and in particular on the crystallinity. By in-situ X-ray diffraction studies of isochronal and isothermal annealing of amorphous films with different thickness at different temperatures it was found that the crystallization process can be quite well described by the Johnson-Mehl-Avrami-Kolmogorov formula modified by the introduction of crystallization onset. This and other parameters of the formula strongly depend on the film thickness. For thickness below about 500 nm the crystallization is very slow. Simultaneously, the appearance and increase of tensile stresses with the annealing time were observed and these stresses were confirmed by detailed studies by both total pattern fitting and sin{sup 2{psi}} method on post-annealed samples. The stresses rapidly increase with decreasing thickness of the films. It seems that there is a strong correlation between the stresses and crystallization onset and/or crystallization rate. Tensile stresses that are generated during crystallization further inhibit crystallization and cause significant thickness dependence of the crystallization. The temperature and time dependence of microstructure of crystallized amorphous films differ significantly from those obtained for as-deposited nanocrystalline films or nanocrystalline powders. During annealing, quite large crystallites are formed quickly with the preferred orientation (001) that is suppressed with the proceeding time.

  14. X-ray diffraction with novel geometry

    Energy Technology Data Exchange (ETDEWEB)

    Prokopiou, Danae [Department of Engineering and Applied Science Cranfield University, Shrivenham Campus, Swindon (United Kingdom); Rogers, Keith, E-mail: k.d.rogers@cranfield.ac.uk [Department of Engineering and Applied Science Cranfield University, Shrivenham Campus, Swindon (United Kingdom); Evans, Paul; Godber, Simon [Imaging Science Group, School of Science and Technology, Nottingham Trent University Clifton Campus, Nottingham (United Kingdom); Shackel, James [Department of Engineering and Applied Science Cranfield University, Shrivenham Campus, Swindon (United Kingdom); Dicken, Anthony [Imaging Science Group, School of Science and Technology, Nottingham Trent University Clifton Campus, Nottingham (United Kingdom)

    2014-01-21

    An innovative geometry for high efficiency harvesting of diffracted X-rays is explored. Further to previous work where planar samples were fixed normal to the primary axis, this work extends focal construct geometry (FCG), to samples randomly oriented with respect to the incident beam. The effect of independent sample rotation around two axes upon the scattering distributions was investigated in analytical, simulation and empirical manners. It was found that, although the profile of Bragg maxima were modified when the sample was rotated, high intensity diffraction data was still acquired. Modelling produced a good match to the empirical data and it was shown that the distortions caused by sample rotation were not severe and predictable even when sample rotations were large. The implications for this are discussed.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. Crystal structure of the quaternary compound CuTa{sub 2}InTe{sub 4} from X-ray powder diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Delgado, G.E. [Laboratorio de Cristalografia, Departamento de Quimica, Facultad de Ciencias, Universidad de Los Andes, Merida 5101 (Venezuela, Bolivarian Republic of)], E-mail: gerzon@ula.ve; Mora, A.J. [Laboratorio de Cristalografia, Departamento de Quimica, Facultad de Ciencias, Universidad de Los Andes, Merida 5101 (Venezuela, Bolivarian Republic of); Grima-Gallardo, P.; Munoz, M.; Duran, S.; Quintero, M. [Centro de Estudios de Semiconductores, Departamento de Fisica, Facultad de Ciencias, Universidad de Los Andes, Merida 5101 (Venezuela, Bolivarian Republic of)

    2008-09-01

    The crystal structure of the new quaternary compound CuTa{sub 2}InTe{sub 4} was studied using X-ray powder diffraction data. The powder pattern refined by the Rietveld method indicates that this material crystallizes in the tetragonal system with space group I-4-bar 2m (No. 121), Z=2, and unit cell parameters a=6.1963(2) A, c=12.4164(4) A, c/a=2.00 and V=476.72(3) A{sup 3}. The structural and instrumental refinement of 28 parameters led to R{sub p}=10.4%, R{sub wp}=11.1%, R{sub exp}=6.8% and {chi}{sup 2}=2.7 for 96 independent reflections.

  20. Crystallization, preliminary X-ray diffraction and structure solution of MosA, a dihydrodipicolinate synthase from Sinorhizobium meliloti L5-30

    Energy Technology Data Exchange (ETDEWEB)

    Leduc, Yvonne A. [Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5 (Canada); Phenix, Christopher P. [Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C9 (Canada); Puttick, Jennifer; Nienaber, Kurt [Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5 (Canada); Palmer, David R. J. [Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5 (Canada); Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C9 (Canada); Delbaere, Louis T. J., E-mail: louis.delbaere@usask.ca [Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5 (Canada)

    2006-01-01

    MosA from S. meliloti L5-30 has been crystallized in solution with pyruvate and the 2.3 Å resolution structure has been solved by molecular replacement using E. coli dihydrodipicolinate synthase as the model. The structure of MosA, a dihydrodipicolinate synthase and reported methyltransferase from Sinorhizobium meliloti, has been solved using molecular replacement with Escherichia coli dihydrodipicolinate synthase as the model. A crystal grown in the presence of pyruvate diffracted X-rays to 2.3 Å resolution using synchrotron radiation and belonged to the orthorhombic space group C222{sub 1}, with unit-cell parameters a = 69.14, b = 138.87, c = 124.13 Å.

  1. Atomic and electronic structure transformations in SnS2 at high pressures: a joint single crystal X-ray diffraction and DFT study.

    Science.gov (United States)

    Filsø, M Ø; Eikeland, E; Zhang, J; Madsen, S R; Iversen, B B

    2016-03-07

    The layered semiconductor SnS2 spurs much interest for both intercalation and optoelectronic applications. Despite the wealth of research in the field of metal dichalcogenides, the structure-property relationship of this compound remains unclear. Here we present a thorough study combining single-crystal X-ray diffraction and DFT calculations on SnS2 in the pressure range 0 band structure calculations. The calculated narrowing of the band gap is supported by a significant, reversible color change of the single crystal. At 20 GPa, the size of the band gap has decreased from 2.15 to 0.88 eV, and band gap closure is predicted to occur at 33 GPa.

  2. Nano structured materials studied by coherent X-ray diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Gulden, Johannes

    2013-03-15

    Structure determination with X-rays in crystallography is a rapidly evolving field. Crystallographic methods for structure determination are based on the assumptions about the crystallinity of the sample. It is vital to understand the structure of possible defects in the crystal, because they can influence the structure determination. All conventional methods to characterize defects require a modelling through simulated data. No direct methods exist to image the core of defects in crystals. Here a new method is proposed, which will enable to visualize the individual scatterers around and at defects in crystals. The method is based on coherent X-ray scattering. X-rays are perfectly suited since they can penetrate thick samples and buried structures can be investigated Recent developments increased the coherent flux of X-Ray sources such as synchrotrons by orders of magnitude. As a result, the use of the coherent properties of X-rays is emerging as a new aspect of X-ray science. New upcoming and operating X-ray laser sources will accelerate this trend. One new method which has the capacity to recover structural information from the coherently scattered photons is Coherent X-ray Diffraction Imaging (CXDI). The main focus of this thesis is the investigation of the structure and the dynamics of colloidal crystals. Colloidal crystals can be used as a model for atomic crystals in order to understand the growth and defect structure. Despite the large interest in these structures, many details are still unknown.Therefore, it is vital to develop new approaches to measure the core of defects in colloidal crystals. After an introduction into the basics of the field of coherent X-ray scattering, this thesis introduces a novel method, Small Angle Bragg Coherent Diffractive Imaging, (SAB-CDI). This new measurement technique which besides the relevance to colloidal crystals can be applied to a large variety of nano structured materials. To verify the experimental possibilities the

  3. Low temperature redetermination of the glycine sodium nitrate structure by using X-ray single crystal diffraction technique

    Energy Technology Data Exchange (ETDEWEB)

    Nichol, G. S. [Department of Chemistry, University of Arizona, 1306 E University Boulevard, P.O. Box 210041, Tuczon, AZ85721 (United States); Hernandez P, J.; Esparza P, H. E. [Centro de Investigacion en Materiales Avanzados S. C., Miguel de Cervantes Saavedra 120, Complejo Industrial Chihuahua, 31109 Chihuahua (Mexico); Pacheco B, M.; Alvarez R, M. E.; Duarte M, A. [Departamento de Fisica, Universidad de Sonora, Blvd. Luis Encinas y Rosales s/n, 83000 Hermosillo, Sonora (Mexico)]. e-mail: alberto.duarte@cimav.edu.mx

    2008-02-15

    The redetermined structure of glycine sodium nitrate, C{sub 2}H{sub 5}N{sub 2}NaO{sub 5}, at 150 K is reported. The compound has an overall polymeric structure whilst the glycine molecule is found in the zwitterionic form. GSN crystals were characterized by XRD powder diffraction, FTIR, UV-VIS, and DTA-TGA techniques. XRD revealed that GSN have a monoclinic structure and space group Cc. Infrared spectra confirmed that the chemical elements and functional groups are present in the crystals and also collaborated the zwitterionic form of molecule. Ultraviolet-Visible spectra showed a wide optical transparent window in the range of 340-1100 nm, which is a desirable characteristic for nonlinear optics applications. DTA-TGA analysis determined that the material is stable up to 198 C. (Author)

  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. X-ray diffraction imaging of material microstructures

    KAUST Repository

    Varga, Laszlo

    2016-10-20

    Various examples are provided for x-ray imaging of the microstructure of materials. In one example, a system for non-destructive material testing includes an x-ray source configured to generate a beam spot on a test item; a grid detector configured to receive x- rays diffracted from the test object; and a computing device configured to determine a microstructure image based at least in part upon a diffraction pattern of the x-rays diffracted from the test object. In another example, a method for determining a microstructure of a material includes illuminating a beam spot on the material with a beam of incident x-rays; detecting, with a grid detector, x-rays diffracted from the material; and determining, by a computing device, a microstructure image based at least in part upon a diffraction pattern of the x-rays diffracted from the material.

  6. Crystallization and preliminary X-ray diffraction studies of choline-binding protein F from Streptococcus pneumoniae

    Energy Technology Data Exchange (ETDEWEB)

    Molina, Rafael [Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto Química Física Rocasolano, CSIC, Serrano 119, 28006 Madrid (Spain); González, Ana; Moscoso, Miriam; García, Pedro [Departamento de Microbiología Molecular, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid (Spain); Stelter, Meike; Kahn, Richard [Institut de Biologie Structurale J.-P. Ebel CEA CNRS UJF, Laboratoire de Cristallographie Macromoléculaire, 41 Rue Jules Horowitz, 38027 Grenoble CEDEX 1 (France); Hermoso, Juan A., E-mail: xjuan@iqfr.csic.es [Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto Química Física Rocasolano, CSIC, Serrano 119, 28006 Madrid (Spain)

    2007-09-01

    The modular choline-binding protein F (CbpF) from S. pneumoniae has been crystallized by the hanging-drop vapour-diffusion method. A SAD data set from a gadolinium-complex derivative has been collected to 2.1 Å resolution. Choline-binding protein F (CbpF) is a modular protein that is bound to the pneumococcal cell wall through noncovalent interactions with choline moieties of the bacterial teichoic and lipoteichoic acids. Despite being one of the more abundant proteins on the surface, along with the murein hydrolases LytA, LytB, LytC and Pce, its function is still unknown. CbpF has been crystallized using the hanging-drop vapour-diffusion method at 291 K. Diffraction-quality orthorhombic crystals belong to space group P2{sub 1}2{sub 1}2, with unit-cell parameters a = 49.13, b = 114.94, c = 75.69 Å. A SAD data set from a Gd-HPDO3A-derivatized CbpF crystal was collected to 2.1 Å resolution at the gadolinium L{sub III} absorption edge using synchrotron radiation.

  7. 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%.

  8. High Resolution X-Ray Diffraction of Macromolecules with Synchrotron Radiation

    Science.gov (United States)

    Stojanoff, Vivian; Boggon, Titus; Helliwell, John R.; Judge, Russell; Olczak, Alex; Snell, Edward H.; Siddons, D. Peter; Rose, M. Franklin (Technical Monitor)

    2000-01-01

    We recently combined synchrotron-based monochromatic X-ray diffraction topography methods with triple axis diffractometry and rocking curve measurements: high resolution X-ray diffraction imaging techniques, to better understand the quality of protein crystals. We discuss these methods in the light of results obtained on crystals grown under different conditions. These non destructive techniques are powerful tools in the characterization of the protein crystals and ultimately will allow to improve, develop, and understand protein crystal growth. High resolution X-ray diffraction imaging methods will be discussed in detail in light of recent results obtained on Hen Egg White Lysozyme crystals and other proteins.

  9. Crystallization of a fungal lytic polysaccharide monooxygenase expressed from glycoengineered Pichia pastoris for X-ray and neutron diffraction

    Energy Technology Data Exchange (ETDEWEB)

    O' Dell, William B.; Swartz, Paul D.; Weiss, Kevin L.; Meilleur, Flora

    2017-01-19

    Lytic polysaccharide monooxygenases (LPMOs) are carbohydrate-disrupting enzymes secreted by bacteria and fungi that break glycosidic bondsviaan oxidative mechanism. Fungal LPMOs typically act on cellulose and can enhance the efficiency of cellulose-hydrolyzing enzymes that release soluble sugars for bioethanol production or other industrial uses. The enzyme PMO-2 fromNeurospora crassa(NcPMO-2) was heterologously expressed inPichia pastoristo facilitate crystallographic studies of the fungal LPMO mechanism. Diffraction resolution and crystal morphology were improved by expressingNcPMO-2 from a glycoengineered strain ofP. pastorisand by the use of crystal seeding methods, respectively. These improvements resulted in high-resolution (1.20 Å) X-ray diffraction data collection at 100 K and the production of a largeNcPMO-2 crystal suitable for room-temperature neutron diffraction data collection to 2.12 Å resolution.

  10. 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.

  11. Crystallization and preliminary X-ray diffraction studies of Seneca Valley virus-001, a new member of the Picornaviridae family.

    Science.gov (United States)

    Venkataraman, Sangita; Reddy, Seshidhar P; Loo, Jackie; Idamakanti, Neeraja; Hallenbeck, Paul L; Reddy, Vijay S

    2008-04-01

    Seneca Valley Virus-001 (SVV-001) is a newly found species in the Picornaviridae family. SVV-001 is the first naturally occurring nonpathogenic picornavirus observed to mediate selective cytotoxicity towards tumor cells with neuroendocrine cancer features. The nonsegmented (+)ssRNA genome of SVV-001 shares closest sequence similarity to the genomes of the members of the Cardiovirus genus. However, based on the distinct characteristics of the genome organization and other biochemical properties, it has been suggested that SVV-001 represents a new genus, namely 'Senecavirus', in the Picornaviridae family. In order to understand the oncolytic properties of SVV-001, the native virus was crystallized using the hanging-drop vapour-diffusion method. The crystals belonged to space group R3, with unit-cell parameters (in the hexagonal setting) a = b = 311.5, c = 1526.4 A. Although the SVV crystals diffracted to better than 2.3 A resolution, the data quality is acceptable [I/sigma(I) > 2.0] to 2.6 A resolution. The unit-cell volume and the locked rotation-function analysis suggest that six particles could be accommodated in the unit cell, with two distinct sets of one third of a particle, each containing 20 protomers, occupying the crystallographic asymmetric unit. (ClinicalTrials.gov identifier NCT00314925)

  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. 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.

  14. 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.

  15. 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.

  16. 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.

  17. Elimination of X-Ray Diffraction through Stimulated X-Ray Transmission.

    Science.gov (United States)

    Wu, B; Wang, T; Graves, C E; Zhu, D; Schlotter, W F; Turner, J J; Hellwig, O; Chen, Z; Dürr, H A; Scherz, A; Stöhr, J

    2016-07-08

    X-ray diffractive imaging with laterally coherent x-ray free-electron laser (XFEL) pulses is increasingly utilized to obtain ultrafast snapshots of matter. Here we report the amazing disappearance of single-shot charge and magnetic diffraction patterns recorded with resonantly tuned, narrow bandwidth XFEL pulses. Our experimental results reveal the exquisite sensitivity of single-shot charge and magnetic diffraction patterns of a magnetic film to the onset of field-induced stimulated elastic x-ray forward scattering. The loss in diffraction contrast, measured over 3 orders of magnitude in intensity, is in remarkable quantitative agreement with a recent theory that is extended to include diffraction.

  18. 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.

  19. 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

  20. X-ray diffraction and the beginnings of X-ray crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Juretschke, H.J. [Polytechnic Univ., Brooklyn, NY (United States)

    1995-12-31

    A retelling of the discovery of X-ray diffraction in Munich in 1912, and an overview of its rapidity spreading applications to crystal structure determination. The early work by Laue`s group and by approaches and different instrumentation, soon set two basic patterns of investigations in this field, with Ewald offering a grand theoretical framework for encompassing both. Some of the successes, problems, and interplays of these trends are reviewed, also as reflected in the stimulation and response by other early participants in structural research, as well as by the interruptions caused by the first World War.

  1. Intergrown new zeolite beta polymorphs with interconnected 12-ring channels solved by combining electron crystallography and single-crystal X-ray diffraction

    KAUST Repository

    Yu, Zhengbao

    2012-10-09

    Two new polymorphs of zeolite beta, denoted as SU-78A and SU-78B, were synthesized by employing dicyclohexylammonium hydroxides as organic structure-directing agents. The structure was solved by combining transmission electron microscopy and single-crystal X-ray diffraction. SU-78 is an intergrowth of SU-78A and SU-78B and contains interconnected 12-ring channels in three directions. The two polymorphs are built from the same building layer, similar to that for the zeolite beta family. The layer stacking in SU-78, however, is different from those in zeolite beta polymorph A, B, and C, showing new zeolite framework topologies. SU-78 is thermally stable up to 600 °C. © 2012 American Chemical Society.

  2. 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

  3. Antisolvent crystallization of pharmaceutical excipients from aqueous solutions and the use of preferred orientation in phase identification by powder X-ray diffraction.

    Science.gov (United States)

    Crisp, J L; Dann, S E; Blatchford, C G

    2011-04-18

    Crystallization of lactose from 10% (w/v) aqueous solutions was investigated with the use of polar antisolvents. Crystal growth was observed at 50-65% antisolvent content and showed a morphological transition from a polyhedral to needle-like habit with increasing antisolvent content, which coincided with a polymorphic transition from alpha lactose monohydrate (Lα·H(2)O) to beta lactose (Lβ). Where dehydrating antisolvents were employed such as methanol and ethanol, evidence of Lα·H(2)O dehydration to form Lα(S) was also observed at 95% antisolvent content. Powder X-ray diffraction (PXRD) analysis of the crystals highlighted the preferred orientation effects exhibited by large crystals of this kind, indicating the difficulties experienced by the non-specialist when performing phase identification of lactose polymorphs. The same studies were applied to raffinose pentahydrate, trehalose dihydrate and mannitol to assess the effects of crystallization conditions on other pharmaceutical excipients. Copyright © 2011 Elsevier B.V. All rights reserved.

  4. Crystal architecture and conformational properties of the inclusion complex, neohesperidin dihydrochalcone-cyclomaltoheptaose (beta-cyclodextrin), by X-ray diffraction.

    Science.gov (United States)

    Malpezzi, Luciana; Fronza, Giovanni; Fuganti, Claudio; Mele, Andrea; Brückner, Sergio

    2004-08-23

    The crystal structure of the host-guest noncovalent complex of cyclomaltoheptaose (beta-cyclodextrin, betaCD) with the O-diglycosyl flavonoid neohesperidin dihydrochalcone [(3,5-dihydroxy-4-(3-hydroxy-4-methoxyhydrocinnamoyl)phenyl-2-O-(alpha-L-rhamnopyranosyl)-beta-D-glucopyranoside, NDC] has been determined from single-crystal X-ray diffraction data collected at low temperature (130 K), using synchrotron radiation. The crystal data are as follows: a =15.125(5), b =30.523(5), c =41.332(5) Angstroms, orthorhombic, space group C222(1). The structure contains 19 molecules of water, of which 11 appeared well positioned, whereas 9 are disordered over 23-positions. The betaCD-NDC complex is characterized by one aromatic part of NDC deeply inserted into the hydrophobic cavity of the betaCD through the primary OH rim, and it is present in the crystal as a dimer. The dimeric units, formed by head-to-head assemblies of CD molecules, each with its guest, are self-assembled in columns. The stability of the columns is provided by host-guest and guest-guest attractive interactions, thus showing a key role of the guest molecules in the crystal architecture. The guest conformation in the complex is different from that reported in the literature for uncomplexed NDC. The host-induced conformational changes on NDC provide the optimum geometry requirements for the assembly of the dimeric units.

  5. Purification, partial characterization, crystallization and preliminary X-ray diffraction of a novel cardiotoxin-like basic protein from Naja naja atra (South Anhui) venom

    Energy Technology Data Exchange (ETDEWEB)

    Rong, Hui; Li, Yan; Lou, Xiao-hua; Zhang, Xio; Gao, Yong-xiang; Teng, Mai-kun, E-mail: mkteng@ustc.edu.cn; Niu, Li-wen, 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)

    2007-02-01

    A novel cardiotoxin-like basic protein from Naja naja atra was crystallized and diffraction data were collected to 2.35 Å resolution. A novel cardiotoxin-like basic protein was isolated from the venom of the Chinese cobra (Naja naja atra) from the south of Anhui in China. The protein inhibits the expression of vascular endothelial growth factor and basic fibroblast growth factor in human lung cancer cell line H1299 and induces the haemolysis of rabbit erythrocytes under low-lecithin conditions. After a two-step chromatographic purification, the resultant 7 kDa protein was crystallized by the hanging-drop vapour-diffusion method at room temperature. A complete data set was collected to 2.35 Å resolution using an in-house X-ray diffraction system. The crystal belongs to space group P4{sub 1}2{sub 1}2, with unit-cell parameters a = b = 43.2, c = 147.9 Å. There are two molecules in the crystallographic asymmetric unit.

  6. 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.

  7. Crystallization and preliminary X-ray diffraction studies of trypsin-like proteases from the gastric fluid of the marine crab Cancer pagurus

    Energy Technology Data Exchange (ETDEWEB)

    Hehemann, Jan-Hendrik [Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg (Germany); Redecke, Lars [Center of Experimental Medicine, Institute of Biochemistry and Molecular Biology I, University Hospital Hamburg-Eppendorf, c/o DESY, 22603 Hamburg (Germany); Perbandt, Markus [Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg (Germany); Saborowski, Reinhard [Biologische Anstalt Helgoland, Alfred Wegener Institute for Polar and Marine Research, 27483 Helgoland (Germany); Betzel, Christian, E-mail: betzel@unisgi1.desy.de [Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg (Germany)

    2007-03-01

    Two trypsins from the gastric fluid of the marine crab C. pagurus were purified and crystallized and X-ray data were collected to 0.97 and 3.2 Å resolution. The digestive fluid of the marine crab Cancer pagurus (Decapoda, Brachyura) contains highly stable proteases which display enhanced activity in aqueous mixtures of organic solvents. Three trypsins were isolated from the gastric fluid and two of them, C.p.TryII and C.p.TryIII, were purified to homogeneity by anion-exchange chromatography and crystallized by hanging-drop vapour diffusion. Diffraction data were collected at a synchrotron to 0.97 and 3.2 Å resolution, respectively. The crystal of C.p.TryII belongs to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 52.06, b = 62.00, c = 71.66 Å. Based on the Matthews coefficient, one protein molecule per asymmetric unit is suggested. In contrast, crystals of C.p.TryIII, which belong to the cubic space group P2{sub 1}3 with unit-cell parameters a = b = c = 215.4 Å, are assumed to contain 12 molecules per asymmetric unit.

  8. 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.

  9. Crystallization and preliminary X-ray diffraction of human interleukin-7 bound to unglycosylated and glycosylated forms of its α-receptor

    Energy Technology Data Exchange (ETDEWEB)

    Wickham, Joseph Jr; Walsh, Scott T. R., E-mail: walsh.220@osu.edu [Department of Molecular and Cellular Biochemistry, Comprehensive Cancer Center, Ohio State University, 467 Hamilton Hall, 1645 Neil Avenue, Columbus, OH 43210 (United States)

    2007-10-01

    Bacterial and insect cell expression systems have been developed to produce unglycosylated and glycosylated forms of human interleukin-7 (IL-7) and the extracellular domain of its α receptor, IL-7Rα. We report the crystallization and X-ray diffraction of IL-7 complexes to both unglycosylated and glycosylated forms of the IL-7Rα to 2.7 and 3.0 Å, respectively. The interleukin-7 (IL-7) signaling pathway plays an essential role in the development, proliferation and homeostasis of T and B cells in cell-mediated immunity. Understimulation and overstimulation of the IL-7 signaling pathway leads to severe combined immunodeficiency, autoimmune reactions, heart disease and cancers. Stimulation of the IL-7 pathway begins with IL-7 binding to its α-receptor, IL-7Rα. Protein crystals of unglycosylated and glycosylated complexes of human IL-7–IL-7Rα extracellular domain (ECD) obtained using a surface entropy-reduction approach diffract to 2.7 and 3.0 Å, respectively. Anomalous dispersion methods will be used to solve the unglycosylated IL-7–IL-7Rα ECD complex structure and this unglycosylated structure will then serve as a model in molecular-replacement attempts to solve the structure of the glycosylated IL-7–α-receptor complex.

  10. 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.

  11. Characterization of X-Ray Diffraction System with a Microfocus X-Ray Source and a Polycapillary Optic

    Science.gov (United States)

    Gubarev, Mikhail; Marshall, Joy K.; Ciszak, Ewa; Ponomarev, Igor

    2000-01-01

    We present here an optimized microfocus x-ray source and polycapillary optic system designed for diffraction of small protein crystals. The x-ray beam is formed by a 5.5mm focal length capillary collimator coupled with a 40 micron x-ray source operating at 46Watts. Measurements of the x-ray flux, the divergence and the spectral characteristics of the beam are presented, This optimized system provides a seven fold greater flux than our recently reported configuration [M. Gubarev, et al., J. of Applied Crystallography (2000) 33, in press]. We now make a comparison with a 5kWatts rotating anode generator (Rigaku) coupled with confocal multilayer focusing mirrors (Osmic, CMF12- 38Cu6). The microfocus x-ray source and polycapillary collimator system delivers 60% of the x-ray flux from the rotating anode system. Additional ways to improve our microfocus x-ray system, and thus increase the x-ray flux will be discussed.

  12. 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.

  13. 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°.

  14. Thermal expansion behavior of empressite, AgTe: A structural study by means of in situ high-temperature single-crystal X-ray diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Bindi, Luca [Museo di Storia Naturale, sez. di Mineralogia, Universita di Firenze, Via La Pira 4, I-50121 Firenze (Italy)], E-mail: luca.bindi@unifi.it

    2009-04-03

    The crystal structure of empressite, AgTe, a rare silver telluride, has been investigated by in situ X-ray single-crystal diffraction methods within the temperature range 298-463 K. AgTe remains orthorhombic, space group Pmnb (Pnma as standard), and shows only normal thermal expansion over the entire temperature range. The unit-cell parameters show a gradual increase with the increase of temperature. Slight adjustments in the geometry of Ag-tetrahedra and in the crystal-chemical environment of tellurium atoms occur in a continuous way without abrupt structural changes. The coefficients of thermal expansion along various axes are: {alpha}{sub a} = 1.5 x 10{sup -5} K{sup -1}, {alpha}{sub b} = 3.0 x 10{sup -5} K{sup -1}, {alpha}{sub c} = 2.2 x 10{sup -5} K{sup -1}, and the bulk thermal expansion coefficient {alpha}{sub V} is 5.4 x 10{sup -5} K{sup -1} for the temperature range 298-463 K.

  15. The discovery of X-rays diffraction: From crystals to DNA. A case study to promote understanding of the nature of science and of its interdisciplinary character

    Science.gov (United States)

    Guerra, Francesco; Leone, Matteo; Robotti, Nadia

    2016-05-01

    The advantages of introducing history of science topics into the teaching of science has been advocated by a large number of scholars within the science education community. One of the main reasons given for using history of science in teaching is its power to promote understanding of the nature of science (NOS). In this respect, the historical case of X-rays diffraction, from the discovery of Max von Laue (1912) to the first X-rays diffraction photographs of DNA (1953), is a case in point for showing that a correct experimental strategy and a favourable theoretical context are not enough to make a scientific discovery.

  16. X-Ray-Diffraction Tests Of Irradiated Electronic Devices: II

    Science.gov (United States)

    Shaw, David C.; Lowry, Lynn E.; Barnes, Charles E.

    1993-01-01

    Report describes research on use of x-ray diffraction to measure stresses in metal conductors of complementary metal oxide/semiconductor (CMOS) integrated circuits exposed to ionizing radiation. Expanding upon report summarized in "X-Ray-Diffraction Tests Of Irradiated Electronic Devices: I" (NPO-18803), presenting data further suggesting relationship between electrical performances of circuits and stresses and strains in metal conductors.

  17. 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...

  18. High pressure x-ray diffraction techniques with synchrotron radiation

    Science.gov (United States)

    Jing, Liu

    2016-07-01

    This article summarizes the developments of experimental techniques for high pressure x-ray diffraction (XRD) in diamond anvil cells (DACs) using synchrotron radiation. Basic principles and experimental methods for various diffraction geometry are described, including powder diffraction, single crystal diffraction, radial diffraction, as well as coupling with laser heating system. Resolution in d-spacing of different diffraction modes is discussed. More recent progress, such as extended application of single crystal diffraction for measurements of multigrain and electron density distribution, time-resolved diffraction with dynamic DAC and development of modulated heating techniques are briefly introduced. The current status of the high pressure beamline at BSRF (Beijing Synchrotron Radiation Facility) and some results are also presented. Project supported by the National Natural Science Foundation of China (Grant Nos. 10875142, 11079040, and 11075175). The 4W2 beamline of BSRF was supported by the Chinese Academy of Sciences (Grant Nos. KJCX2-SW-N20, KJCX2-SW-N03, and SYGNS04).

  19. Ultrafast X-Ray Diffraction of Heterogeneous Solid Hydrogen

    Energy Technology Data Exchange (ETDEWEB)

    Levitan, Abraham [Olin College of Engineering, Needham, MA (United States)

    2015-08-19

    Angularly resolved x-ray diffraction at 5.5 keV establishes the structure of a 5 µm diameter solid hydrogen jet, providing a foundation for analysis of hydrogen in a warm dense matter state. The jet was composed of approximately 65 % ± 5% HCP and 35 % ± 5% FCC by volume with an average crystallite size on the order of hundreds of nanometers. Broadening in the angularly resolved spectrum provided strong evidence for anisotropic strain up to approximately 3 % in the HCP lattice. Finally, we found no evidence for orientational ordering of the crystal domains.

  20. Ab initio structure determination via powder X-ray diffraction

    Indian Academy of Sciences (India)

    Digamber G Porob; T N Guru Row

    2001-10-01

    Structure determination by powder X-ray diffraction data has gone through a recent surge since it has become important to get to the structural information of materials which do not yield good quality single crystals. Although the method of structure completion when once the starting model is provided is facile through the Rietveld refinement technique, the structure solution ab initio os still not push-button technology. In this article a survey of the recent development in this area is provided with an illustration of the structure determination of -NaBi3V2O10.

  1. Aspherical-atom modeling of coordination compounds by single-crystal X-ray diffraction allows the correct metal atom to be identified.

    Science.gov (United States)

    Dittrich, Birger; Wandtke, Claudia M; Meents, Alke; Pröpper, Kevin; Mondal, Kartik Chandra; Samuel, Prinson P; Amin Sk, Nurul; Singh, Amit Pratap; Roesky, Herbert W; Sidhu, Navdeep

    2015-02-02

    Single-crystal X-ray diffraction (XRD) is often considered the gold standard in analytical chemistry, as it allows element identification as well as determination of atom connectivity and the solid-state structure of completely unknown samples. Element assignment is based on the number of electrons of an atom, so that a distinction of neighboring heavier elements in the periodic table by XRD is often difficult. A computationally efficient procedure for aspherical-atom least-squares refinement of conventional diffraction data of organometallic compounds is proposed. The iterative procedure is conceptually similar to Hirshfeld-atom refinement (Acta Crystallogr. Sect. A- 2008, 64, 383-393; IUCrJ. 2014, 1,61-79), but it relies on tabulated invariom scattering factors (Acta Crystallogr. Sect. B- 2013, 69, 91-104) and the Hansen/Coppens multipole model; disordered structures can be handled as well. Five linear-coordinate 3d metal complexes, for which the wrong element is found if standard independent-atom model scattering factors are relied upon, are studied, and it is shown that only aspherical-atom scattering factors allow a reliable assignment. The influence of anomalous dispersion in identifying the correct element is investigated and discussed.

  2. Energy-dispersive X-ray diffraction mapping on a benchtop X-ray fluorescence system

    OpenAIRE

    Lane, D W.; Nyombi, A.; Shackel, J.

    2014-01-01

    A method for energy-dispersive X-ray diffraction mapping is presented, using a conventional low-power benchtop X-ray fluorescence spectrometer, the Seiko Instruments SEA6000VX. Hyper spectral X-ray maps with a 10µm step size were collected from polished metal surfaces, sectioned Bi, Pb and steel shot gun pellets. Candidate diffraction lines were identified by eliminating those that matched a characteristic line for an element and those predicted for escape peaks, sum peaks, and Rayleigh and C...

  3. Resolution of crystal structures by X-ray and neutrons powder diffraction using global optimisation methods; Resolution des structures cristallines par diffraction des rayons X et neutrons sur poudres en utilisant les methodes d'optimisation globale

    Energy Technology Data Exchange (ETDEWEB)

    Palin, L

    2005-03-15

    We have shown in this work that X-ray diffraction on powder is a powerful tool to analyze crystal structure. The purpose of this thesis is the resolution of crystal structures by X-ray and neutrons diffraction on powder using global optimisation methods. We have studied 3 different topics. The first one is the order-disorder phenomena observed in some globular organic molecular solids. The second is the opiate family of neuropeptides. These neurotransmitters regulate sensory functions including pain and control of respiration in the central nervous system. The aim of our study was to try to determine the crystal structure of Leu-enkephalin and some of its sub-fragments. The determination of the crystal structures has been done performing Monte Carlo simulations. The third one is the location of benzene in a sodium-X zeolite. The zeolite framework was already known and the benzene has been localized by simulated annealing and by the use of maximum entropy maps.

  4. 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%.

  5. Individual phase constitutive properties of a TRIP-assisted QP980 steel from a combined synchrotron X-ray diffraction and crystal plasticity approach

    Energy Technology Data Exchange (ETDEWEB)

    Hu, X. H.; Sun, X.; Hector, L. G.; Ren, Y.

    2017-06-01

    Microstructure-based constitutive models for multiphase steels require accurate constitutive properties of the individual phases for component forming and performance simulations. We address this requirement with a combined experimental/theoretical methodology which determines the critical resolved shear stresses and hardening parameters of the constituent phases in QP980, a TRIP assisted steel subject to a two-step quenching and partitioning heat treatment. High energy X-Ray diffraction (HEXRD) from a synchrotron source provided the average lattice strains of the ferrite, martensite, and austenite phases from the measured volume during in situ tensile deformation. The HEXRD data was then input to a computationally efficient, elastic-plastic self-consistent (EPSC) crystal plasticity model which estimated the constitutive parameters of different slip systems for the three phases via a trial-and-error approach. The EPSC-estimated parameters are then input to a finite element crystal plasticity (CPFE) model representing the QP980 tensile sample. The predicted lattice strains and global stress versus strain curves are found to be 8% lower that the EPSC model predicted values and from the HEXRD measurements, respectively. This discrepancy, which is attributed to the stiff secant assumption in the EPSC formulation, is resolved with a second step in which CPFE is used to iteratively refine the EPSC-estimated parameters. Remarkably close agreement is obtained between the theoretically-predicted and experimentally derived flow curve for the QP980 material.

  6. Fe^2^+-Mg Order-Disorder Processes in Orthopyroxenes from São João Nepomuceno (IVA) Iron Meteorite: ^57Fe Mössbauer Spectroscopy and Single-Crystal X-Ray Diffraction Studies

    Science.gov (United States)

    Dos Santos, E.; Scorzelli, R. B.; Abdu, Y. A.; Varela, M. E.; Munayco, P.

    2013-09-01

    Here we study cation distribution in orthopyroxenes from São João Nepomuceno meteorite by Mössbauer spectroscopy, electron microprobe and single-crystal X-ray diffraction, in order to get insights into the thermal history of this meteorite.

  7. 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.

  8. X-ray diffraction contrast tomography (DCT) system, and an X-ray diffraction contrast tomography (DCT) method

    DEFF Research Database (Denmark)

    2012-01-01

    Source: US2012008736A An X-ray diffraction contrast tomography system (DCT) comprising a laboratory X-ray source (2), a staging device (5) rotating a polycrystalline material sample in the direct path of the X-ray beam, a first X-ray detector (6) detecting the direct X-ray beam being transmitted ...... in the polycrystalline sample is determined based on the two-dimensional position of extinction spots and the associated angular position of the sample for a set of extinction spots pertaining to the individual grain....

  9. 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.

  10. In-situ observation of zinc electrodeposition on iron single crystal using synchrotron radiation x-ray diffraction

    CERN Document Server

    Kurosaki, M; Kawasaki, K

    2002-01-01

    Continuous in-situ observations of changes in crystal orientation during zinc electrodeposition were performed using novel electrolysis cell that secure uniform current distribution through thin electrolyte layer. It has been clarified that electrodeposition can be separated into the two regions. First one is epitaxial deposition region in which orientations of deposited zinc and substrate keep following relations; Fe(100)//Zn(10 centre dot 1) Fe(110)//Zn(00 centre dot 2), Fe(111)//Zn(00 centre dot 2). This region continued until the thickness of the deposit became about 0.5 mu m. Second one is bulk deposition region, in which the overpotential settled by electrolysis conditions determines the crystal orientation. Low overpotential leads to promoting Zn(00 centre dot 2) deposition, and higher overpotential Zn(10 centre dot 1) and Zn(11 centre dot 0). Influences of the current density changes on the crystal orientation were also clarified. The use of an adsorbing organic additive influences both on the epitaxi...

  11. 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.

  12. Crystallization and preliminary X-ray diffraction studies of two thermostable α-galactosidases from glycoside hydrolase family 36

    Energy Technology Data Exchange (ETDEWEB)

    Foucault, M. [Institut de Biologie et Chimie des Protéines, CNRS-UCBL, UMR 5086, Laboratoire de Bio-Cristallographie IFR128 ‘BioSciences Lyon-Gerland’, 7 Passage du Vercors, 69367 Lyon CEDEX 07 (France); Watzlawick, H.; Mattes, R. [Institut für Industrielle Genetik, Universität Stuttgart, Allmandring 31, D-70569 Stuttgart (Germany); Haser, R.; Gouet, P., E-mail: p.gouet@ibcp.fr [Institut de Biologie et Chimie des Protéines, CNRS-UCBL, UMR 5086, Laboratoire de Bio-Cristallographie IFR128 ‘BioSciences Lyon-Gerland’, 7 Passage du Vercors, 69367 Lyon CEDEX 07 (France)

    2006-02-01

    The α-galactosidases AgaA, AgaB and AgaA A355E mutant from Geobacillus stearothermophilus have been overexpressed in Escherichia coli. Crystals of AgaB and AgaA A355E have been obtained by the vapour-diffusion method and synchrotron data have been collected to 2.0 and 2.8 Å resolution, respectively. α-Galactosidases from thermophilic organisms have gained interest owing to their applications in the sugar industry. The α-galactosidases AgaA, AgaB and AgaA A355E mutant from Geobacillus stearothermophilus have been overexpressed in Escherichia coli. Crystals of AgaB and AgaA A355E have been obtained by the vapour-diffusion method and synchrotron data have been collected to 2.0 and 2.8 Å resolution, respectively. Crystals of AgaB belong to space group I222 or I2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 87.5, b = 113.3, c = 161.6 Å. Crystals of AgaA A355E belong to space group P3{sub 1}21 or P3{sub 2}21, with unit-cell parameters a = b = 150.1, c = 233.2 Å.

  13. Anomalous X-ray Diffraction Studies for Photovoltaic Applications

    Energy Technology Data Exchange (ETDEWEB)

    2011-06-22

    Anomalous X-ray Diffraction (AXRD) has become a useful technique in characterizing bulk and nanomaterials as it provides specific information about the crystal structure of materials. In this project we present the results of AXRD applied to materials for photovoltaic applications: ZnO loaded with Ga and ZnCo{sub 2}O{sub 4} spinel. The X-ray diffraction data collected for various energies were plotted in Origin software. The peaks were fitted using different functions including Pseudo Voigt, Gaussian, and Lorentzian. This fitting provided the integrated intensity data (peaks area values), which when plotted as a function of X-ray energies determined the material structure. For the first analyzed sample, Ga was not incorporated into the ZnO crystal structure. For the ZnCo{sub 2}O{sub 4} spinel Co was found in one or both tetrahedral and octahedral sites. The use of anomalous X-ray diffraction (AXRD) provides element and site specific information for the crystal structure of a material. This technique lets us correlate the structure to the electronic properties of the materials as it allows us to probe precise locations of cations in the spinel structure. What makes it possible is that in AXRD the diffraction pattern is measured at a number of energies near an X-ray absorption edge of an element of interest. The atomic scattering strength of an element varies near its absorption edge and hence the total intensity of the diffraction peak changes by changing the X-ray energy. Thus AXRD provides element specific structural information. This method can be applied to both crystalline and liquid materials. One of the advantages of AXRD in crystallography experiments is its sensitivity to neighboring elements in the periodic tables. This method is also sensitive to specific crystallographic phases and to a specific site in a phase. The main use of AXRD in this study is for transparent conductors (TCs) analysis. TCs are considered to be important materials because of their

  14. Time-resolved synchrotron x-ray diffraction studies of the crystallization of amorphous Co(80-x)FexB₂₀

    Energy Technology Data Exchange (ETDEWEB)

    Simmons, L. M., E-mail: l.simmons@mmu.ac.uk [Division of Electrical and Electronic Engineering, School of Engineering, Manchester Metropolitan University, Manchester M1 5GD (United Kingdom); Greig, D. [School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT (United Kingdom); Lucas, C. A. [Oliver Lodge Laboratory, Department of Physics, University of Liverpool, Liverpool L69 7ZE (United Kingdom); Kilcoyne, S. H. [School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH (United Kingdom)

    2014-09-28

    This paper addresses the time-dependent crystallization process occurring in “bulk” amorphous Co(80-x)FexB₂₀ (x = 20, 40) metallic ribbons by means of synchrotron x-ray diffraction (SXRD) and transmission electron microscopy. Metallic ribbons, produced via melt-spinning technique, were annealed in-situ, with SXRD patterns collected every 60 s. SXRD reveals that Co₄₀Fe₄₀B₂₀ alloys crystallize from an amorphous structure to a primary bcc α-(Co,Fe) phase, whereas Co₆₀Fe₂₀B₂₀ initially crystallizes into the same bcc α-(Co,Fe) but exhibits cooperative growth of both stable and metastable boride phases later into the hold. Johnson-Mehl-Avrami-Kolmogorov statistics was used on post annealed samples to determine the mechanisms of growth and the activation energy (Ea) of the α-(Co,Fe) phase. Results indicate that the growth mechanisms are similar for both alloy compositions for all annealing temperatures, with the Avrami exponent of n = 1.51(1) and 2.02(6) for x = 20 and 40, respectively, suggesting one-dimensional growth, with a decreasing nucleation rate. Activation energy for α-(Co,Fe) was determined to be 2.7(1) eV and 2.4(3) eV in x = 20 and 40, respectively, suggesting that those alloys with a lower Co content have a stronger resistance to crystallization. Based on these results, fabrication of CoFeB magnetic tunnel junctions via depositing amorphous layers and subsequently annealing to induce lattice matching presents itself as a viable and efficient method, for increasing the giant magnetoresistance in magnetic tunnel junctions.

  15. Crystallization and X-ray diffraction of 5'-fluoro-5'-deoxyadenosine synthase, a fluorination enzyme from Streptomyces cattleya.

    Science.gov (United States)

    Dong, Changjiang; Deng, Hai; Dorward, Mark; Schaffrath, Christoph; O'Hagan, David; Naismith, James H

    2003-12-01

    Organofluorine compounds are widely prepared throughout the chemicals industry, but their prepararion generally requires harsh fluorinating reagents and non-aqueous solvents. On the other hand, biology has hardly exploited organofluorine compounds. A very few organisms synthesize organofluorine metabolites, suggesting they have evolved a mechanism to overcome the kinetic desolvation barrier to utilizing F(-)(aq). Here, the purification and crystallization of an enzyme from Streptomyces cattleya which is responsible for the synthesis of the C-F bond during fluoroacetate and 4-fluorothreonine biosynthesis is reported. The protein crystallizes in space group C222(1), with unit-cell parameters a = 75.9, b = 130.3, c = 183.4 A, alpha = beta = gamma = 90 degrees. Data were recorded to 1.9 A at the ESRF. The structure of the protein should provide important insights into the biochemical process of C-F bond formation.

  16. High-pressure single-crystal X-ray diffraction study on Super Fluorous Phase B up to 7.4 GPa

    Science.gov (United States)

    Kuribayashi, T.; Kojitani, H.; Nagase, T.; Akaogi, M.; Mao, H.; Hemley, R.; Kudoh, Y.

    2008-12-01

    Super hydrous phase B (SUP-B), Mg10Si3O14(OH)4, is known as one of dense hydrous magnesium silicate minerals (DHMS). Also, super fluorous phase B (sup-B-F), Mg10Si3O14F4, was firstly synthesized by Hazen et al. (1997). In the crystal structure of SUP-B-F, F replaces OH in sup-B structure. Therefore, differences of behavior between SUP-B-F and SUP-B under high-pressure conditions directory reflect the effect of hydrogen bonding. In this study, to clarify the behavior of SUP-B-F under high-pressure condition, SUP-B-F was synthesized at 21 GPa and 1400°C conditions using the Kawai type multi anvil apparatus installed in Gakushu-in University. Using a synthesized single-crystal (0.04 × 0.04 × 0.03 mm3), high-pressure single-crystal X-ray diffraction measurements were conducted up to 7.4 GPa with synchrotron radiation. Lattice constants were determined at several pressure points up to 7.4 GPa. The isothermal bulk modulus of SUP-B-F, calculated from the Birch-Murnaghan Equation of State, was 154(2) GPa with a pressure derivative K'=4 (assuming). This value is significantly larger than that of super hydrous phase B (142.8(5) GPa with K"f=5.7 by Crichton et al., 1999). The X-ray reflection intensity data set was collected at 5.0 GPa using the four-circle diffractometer installed at the beam line BL-10A in Photon Factory, Japan. 198 reflections were used for structure refinement (the number of measured reflections is 786). After Lorentz- polarization correction and background reduction were applied for all intensity data, the crystallographic equivalent reflections (Orthorhombic, Pnnm) were averaged. Structure refinement results were R=5.0% and wR2=13.1%, respectively.

  17. X-ray diffraction properties of highly oriented pyrolytic graphite

    Energy Technology Data Exchange (ETDEWEB)

    Freund, A.K.; Munkholm, A.; Brennan, S. [Stanford Synchrotron Radiation Lab., CA (United States)

    1996-12-31

    The x-ray diffraction properties of highly oriented pyrolytic graphite (HOPG) were studied for x-ray energies ranging from 4 to 60 keV. In particular, the secondary extinction thickness was determined by recording the peak and integrated reflectivity as a function of depth below the surface. The results showed that for the high quality material investigated a thickness of 200 to 300 {micro}m was sufficient to get 80% of the maximum reflectivity that is obtained for a very thick plate. Primary extinction was important for low energy and still persisted at higher energies. Inhomogeneities of the mosaic structure were observed, too, that make this material not a truly ideal mosaic monochromator crystal. However, quite high peak reflectivities between 35% and 58% were measured at FWHM of 0.25 to 0.45 degrees. A 200 {micro}m thick plate was then prepared and glued on a bending device to manufacture a monochromator or analyzer with variable curvature that works from flat down to a minimum bending radius of 10 cm. The successful tests of this device confirmed that HOPG plates much thinner than those commonly used as x-ray monochromators and analyzers still have high efficiency and can be curved to achieve dynamical focusing.

  18. Redetermination of eveite, Mn2AsO4(OH), based on single-crystal X-ray diffraction data

    Science.gov (United States)

    Yang, Yongbo W.; Stevenson, Ryan A.; Siegel, Alesha M.; Downs, Gordon W.

    2011-01-01

    The crystal structure of eveite, ideally Mn2(AsO4)(OH) [dimanganese(II) arsenate(V) hydroxide], was refined from a single crystal selected from a co-type sample from Långban, Filipstad, Varmland, Sweden. Eveite, dimorphic with sarkinite, is structurally analogous with the important rock-forming mineral andalusite, Al2OSiO4, and belongs to the libethenite group. Its structure consists of chains of edge-sharing distorted [MnO4(OH)2] octa­hedra (..2 symmetry) extending parallel to [001]. These chains are cross-linked by isolated AsO4 tetra­hedra (..m symmetry) through corner-sharing, forming channels in which dimers of edge-sharing [MnO4(OH)] trigonal bipyramids (..m symmetry) are located. In contrast to the previous refinement from Weissenberg photographic data [Moore & Smyth (1968 ▶). Am. Mineral. 53, 1841–1845], all non-H atoms were refined with anisotropic displacement param­eters and the H atom was located. The distance of the donor and acceptor O atoms involved in hydrogen bonding is in agreement with Raman spectroscopic data. Examination of the Raman spectra for arsenate minerals in the libethenite group reveals that the position of the peak originating from the O—H stretching vibration shifts to lower wavenumbers from eveite, to adamite, zincolivenite, and olivenite. PMID:22199466

  19. Redetermination of eveite, Mn(2)AsO(4)(OH), based on single-crystal X-ray diffraction data.

    Science.gov (United States)

    Yang, Yongbo W; Stevenson, Ryan A; Siegel, Alesha M; Downs, Gordon W

    2011-12-01

    The crystal structure of eveite, ideally Mn(2)(AsO(4))(OH) [dimanganese(II) arsenate(V) hydroxide], was refined from a single crystal selected from a co-type sample from Långban, Filipstad, Varmland, Sweden. Eveite, dimorphic with sarkinite, is structurally analogous with the important rock-forming mineral andalusite, Al(2)OSiO(4), and belongs to the libethenite group. Its structure consists of chains of edge-sharing distorted [MnO(4)(OH)(2)] octa-hedra (..2 symmetry) extending parallel to [001]. These chains are cross-linked by isolated AsO(4) tetra-hedra (..m symmetry) through corner-sharing, forming channels in which dimers of edge-sharing [MnO(4)(OH)] trigonal bipyramids (..m symmetry) are located. In contrast to the previous refinement from Weissenberg photographic data [Moore & Smyth (1968 ▶). Am. Mineral.53, 1841-1845], all non-H atoms were refined with anisotropic displacement param-eters and the H atom was located. The distance of the donor and acceptor O atoms involved in hydrogen bonding is in agreement with Raman spectroscopic data. Examination of the Raman spectra for arsenate minerals in the libethenite group reveals that the position of the peak originating from the O-H stretching vibration shifts to lower wavenumbers from eveite, to adamite, zincolivenite, and olivenite.

  20. Redetermination of eveite, Mn2AsO4(OH, based on single-crystal X-ray diffraction data

    Directory of Open Access Journals (Sweden)

    Yongbo W. Yang

    2011-12-01

    Full Text Available The crystal structure of eveite, ideally Mn2(AsO4(OH [dimanganese(II arsenate(V hydroxide], was refined from a single crystal selected from a co-type sample from Långban, Filipstad, Varmland, Sweden. Eveite, dimorphic with sarkinite, is structurally analogous with the important rock-forming mineral andalusite, Al2OSiO4, and belongs to the libethenite group. Its structure consists of chains of edge-sharing distorted [MnO4(OH2] octahedra (..2 symmetry extending parallel to [001]. These chains are cross-linked by isolated AsO4 tetrahedra (..m symmetry through corner-sharing, forming channels in which dimers of edge-sharing [MnO4(OH] trigonal bipyramids (..m symmetry are located. In contrast to the previous refinement from Weissenberg photographic data [Moore & Smyth (1968. Am. Mineral. 53, 1841–1845], all non-H atoms were refined with anisotropic displacement parameters and the H atom was located. The distance of the donor and acceptor O atoms involved in hydrogen bonding is in agreement with Raman spectroscopic data. Examination of the Raman spectra for arsenate minerals in the libethenite group reveals that the position of the peak originating from the O—H stretching vibration shifts to lower wavenumbers from eveite, to adamite, zincolivenite, and olivenite.

  1. Crystal structure refinement of the ternary compound Cu{sub 2}SnTe{sub 3} by X-ray powder diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Mora, A.J. [Laboratorio de Cristalografia, Departamento de Quimica, Facultad de Ciencias, Universidad de Los Andes, Merida (Venezuela); Marcano, G.; Rincon, C. [Centro de Estudios de Semiconductores, Departamento de Fisica, Facultad de Ciencias, Universidad de Los Andes, Merida (Venezuela); Delgado, G.E.

    2008-04-15

    The ternary compound Cu{sub 2}SnTe{sub 3} crystallizes in the Imm2 (N circle 44) space group, Z=2, with a=2.833(4) A, b=4.274(1) A, c=6.043(1) A, V=331.5(1) A{sup 3}. Its structure was refined from X-ray powder diffraction data using the Rietveld method. The refinement of 25 instrumental and structural variables led to R{sub p}=10.2%, R{sub wp}=11.8%, R{sub exp}=7.7%, R{sub B}=10.6%, S=1.6 and {chi}{sup 2}=2.6, for 5501 step intensities and 163 independent reflections. This compound is isostructural with Cu{sub 2}GeSe{sub 3}, and consists of a three-dimensional arrangement of slightly distorted CuTe{sub 4} and SnTe{sub 4} tetrahedra connected by common corners. (copyright 2008 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  2. Variable-temperature single-crystal X-ray diffraction study of tetragonal and cubic perovskite-type barium titanate phases.

    Science.gov (United States)

    Nakatani, Tomotaka; Yoshiasa, Akira; Nakatsuka, Akihiko; Hiratoko, Tatsuya; Mashimo, Tsutomu; Okube, Maki; Sasaki, Satoshi

    2016-02-01

    A variable-temperature single-crystal X-ray diffraction study of a synthetic BaTiO3 perovskite has been performed over the temperature range 298-778 K. A transition from a tetragonal (P4mm) to a cubic (Pm3m) phase has been revealed near 413 K. In the non-centrosymmetric P4mm symmetry group, both Ti and O atoms are displaced along the c-axis in opposite directions with regard to the Ba position fixed at the origin, so that Ti(4+) and Ba(2+) cations occupy off-center positions in the TiO6 and BaO12 polyhedra, respectively. Smooth temperature-dependent changes of the atomic coordinates become discontinuous with the phase transition. Our observations imply that the cations remain off-center even in the high-temperature cubic phase. The temperature dependence of the mean-square displacements of Ti in the cubic phase includes a significant static component which means that Ti atoms are statistically distributed in the off-center positions.

  3. High-temperature single-crystal X-ray diffraction study of tetragonal and cubic perovskite-type PbTiO3 phases.

    Science.gov (United States)

    Yoshiasa, Akira; Nakatani, Tomotaka; Nakatsuka, Akihiko; Okube, Maki; Sugiyama, Kazumasa; Mashimo, Tsutomu

    2016-06-01

    A high-temperature single-crystal X-ray diffraction study of a synthetic PbTiO3 perovskite was carried out over the wide temperature range 298-928 K. A transition from a tetragonal (P4mm) to a cubic (Pm \\bar 3 m) phase has been revealed near 753 K. In the non-centrosymmetric P4mm symmetry group, the difference in relative displacement between Pb and O along the c-axis is much larger than that between Ti and O. The Pb and Ti cations contribute sufficiently to polarization being shifted in the opposite direction compared with the shift of O atoms. Deviation from the linear changes in Debye-Waller factors and bonding distances in the tetragonal phases can be interpreted as a precursor phenomenon before the phase transition. Disturbance of the temperature factor Ueq for O is observed in the vicinity of the transition point, while Ueq values for Pb and Ti are continuously changing with increasing temperature. The O site includes the clear configurational disorder in the cubic phase. The polar local positional distortions remain in the cubic phase and are regarded as the cause of the paraelectricity. Estimated values of the Debye temperature ΘD for Pb and Ti are 154 and 467 K in the tetragonal phase and decrease 22% in the high-temperature phase. Effective potentials for Pb and Ti change significantly and become soft after the phase transition.

  4. Single-crystal X-ray diffraction study of Fe2SiO4 fayalite up to 31 GPa

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Jin S.; Hu, Yi; Shelton, Hannah; Kung, Jennifer; Dera, Przemyslaw

    2016-10-03

    Olivine is widely believed to be the most abundant mineral in the Earth’s upper mantle. Here, we report structural refinement results for the Fe-end-member olivine, Fe2SiO4 fayalite, up to 31 GPa in diamond-anvil cell, using single-crystal synchrotron X-ray diffraction. Unit-cell parameters a, b, c and V, average Si–O Fe–O bond lengths, as well as Si–O Fe–O polyhedral volumes continuously decrease with increasing pressure. The pressure derivative of isothermal bulk modulus K'T0 is determined to be 4.0 (2) using third-order Birch–Murnaghan equation of state with ambient isothermal bulk modulus fixed to 135 GPa on the basis of previous Brillouin measurements. The Si–O tetrahedron is stiffer than the Fe–O octahedra, and the compression mechanism is dominated by Fe–O bond and Fe–O octahedral compression. Densities of olivine along 1600 and 900 K adiabats are calculated based on this study. The existence of metastable olivine inside the cold subduction slab could cause large positive buoyancy force against subduction, slow down the subduction and possibly affect the slab geometry.

  5. Anharmonic thermal motion of Ag in AgCrSe 2: A high-temperature single-crystal X-ray diffraction study

    Science.gov (United States)

    Van Der Lee, A.; Wiegers, G. A.

    1989-10-01

    The thermal motion of Ag in the two-dimensional silver ion conductor AgCrSe 2 (at 295 K; a = 3.6798(2) Å, c = 21.225(2) Å; Z = 3; spacegroup R3 m) is studied as a function of temperature by single-crystal X-ray diffraction. At room temperature the Ag atoms occupy only one-half of the available tetrahedral holes between the CrSe 2 sandwiches. Disordering of the silver sublattice over all tetrahedral sites proceeds second order with Tc = 475 K: above Tc the spacegroup is R overline3m . Refinements were performed with data measured at six different temperatures in the range 295-673 K. Anharmonic temperature factors of Ag based on the Gram-Charlier expansion have been refined up to fourth order. Rw values range from 0.022 to 0.049, the number of variables from 17 to 22. The refinements confirm the second-order nature of the order-disorder transition. Below Tc the largest thermal vibrations are directed to the octahedral sites between the CrSe 2 sandwiches. The plane between the α- and β-lattice plays a crucial role. The joint probability density function (jpdf) of Ag is high in regions surrounding the projected α- and β-sites and the octahedral site; at these sites the jpdf shows a minimum. The diffusion of Ag from an α- to a β-site proceeds therefore via this intermediate plane.

  6. Crystallization kinetics of Fe-B based amorphous alloys studied in-situ using X-rays diffraction and differential scanning calorimetry

    Directory of Open Access Journals (Sweden)

    Santos D.R. dos

    2001-01-01

    Full Text Available The crystallization processes for the amorphous metallic alloys Fe74B17Si2Ni4Mo3 and Fe86B6Zr7Cu1 (at. % were investigated using X-rays diffraction measurements performed in-situ during Joule-heating, with simultaneous monitoring of the electrical resistance. We determined the main structural transitions and crystalline phases formed during heating, and correlated these results to the observed resistance variations. As the annealing current is increased, the resistance shows an initial decrease due to stress relaxation, followed by a drop to a minimum value due to massive nucleation and growth of alpha-Fe nanocrystals. Further annealing causes the formation of small fractions of Fe-B, B2Zr or ZrO2, while the resistance increases due to temperature enhancement. In situ XRD measurements allowed the identification of metastable phases, as the gamma-Fe phase which occurs at high temperatures. The exothermal peaks observed in the differential scanning calorimetry (DSC for each alloy corroborate the results. We also have performed DSC measurements with several heating rates, which allowed the determination of the Avrami exponent and crystallization activation energy for each alloy. The obtained activation energies (362 and 301 kJ/mol for Fe-B-Zr-Cu; 323 kJ/mol for Fe-B-Si-Ni-Mo are comparable to reported values for amorphous iron alloys, while the Avrami exponent values (n = 1.0 or n = 1.2 are consistent with diffusion controlled crystallization processes with nucleation rates close to zero.

  7. 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.

  8. Effect of non-hydrostatic conditions on the elastic behaviour of magnetite: an in situ single-crystal X-ray diffraction study

    Science.gov (United States)

    Gatta, G. Diego; Kantor, I.; Boffa Ballaran, T.; Dubrovinsky, L.; McCammon, C.

    2007-11-01

    The high-pressure elastic behaviour and the pressure-induced structural evolution of synthetic magnetite were investigated up to 11.11(5) GPa by means of in situ single-crystal X-ray diffraction with a diamond anvil cell, using the mix methanol:ethanol:water = 16:3:1 as pressure-transmitting medium and the ruby-fluorescence method for pressure-calibration. The evolution of the ruby R1-fluorescence line with P, with a drastic increase of the full-width-at-half-maximum (FWHM) of the Lorentzian profile at P > 9 GPa, shows that the P-medium is not hydrostatic above 9 GPa. Such a condition is well reflected by the drastic increase (by 20-22%) of the FWHM of the diffraction peak profiles of magnetite, by the behaviour of the Eulerian finite strain versus normalized pressures plot ( f e - F e plot) and by the slight EoS-misfit. However, the diffraction data collected during decompression showed a reversible/complete restoration of the diffraction profiles and of the elastic behaviour in the f e - F e plot. The reflection conditions dictated by the Fdbar 3m space group confirm that symmetry of magnetite is maintained within the P-range investigated. The structural refinements performed at 0.0001, 4.99(3) and 9.21(8) GPa show that the evolution of the oxygen u-parameter is almost constant within the P-range investigated. A weighted linear regression through the data points gives only a slight negative slope and no discontinuity is observed within the P-range investigated. A similar continuous behaviour is also observed in the evolution of the T- and M-polyhedral volumes, bond distances and angles with P. On the basis of data reported in this study, it appears that the elastic behaviour and the structural evolution of magnetite is drastically influenced by the experimental conditions (i.e., hydrostatic or non-hydrostatic), and diffraction data of magnetite collected under non-hydrostatic conditions are unusable for a reliable description of the elastic behaviour and for the

  9. Characteristic, parametric, and diffracted transition X-ray radiation for observation of accelerated particle beam profile

    Science.gov (United States)

    Chaikovska, I.; Chehab, R.; Artru, X.; Shchagin, A. V.

    2017-07-01

    The applicability of X-ray radiation for the observation of accelerated particle beam profiles is studied. Three types of quasi-monochromatic X-ray radiation excited by the particles in crystals are considered: characteristic X-ray radiation, parametric X-ray radiation, diffracted transition X-ray radiation. Radiation is collected at the right angle to the particle beam direction. It is show that the most intensive differential yield of X-ray radiation from Si crystal can be provided by characteristic radiation at incident electron energies up to tens MeV, by parametric radiation at incident electron energies from tens to hundreds MeV, by diffracted transition X-ray radiation at GeV and multi-GeV electron energies. Therefore these kinds of radiation are proposed for application to beam profile observation in the corresponding energy ranges of incident electrons. Some elements of X-ray optics for observation of the beam profile are discussed. The application of the DTR as a source of powerful tunable monochromatic linearly polarized X-ray beam excited by a multi-GeV electron beam on the crystal surface is proposed.

  10. Single shot diffraction of picosecond 8.7-keV x-ray pulses

    Directory of Open Access Journals (Sweden)

    F. H. O’Shea

    2012-02-01

    Full Text Available We demonstrate multiphoton, single shot diffraction images of x rays produced by inverse Compton scattering a high-power CO_{2} laser from a relativistic electron beam, creating a pulse of 8.7 keV x rays. The tightly focused, relatively high peak brightness electron beam and high photon density from the 2 J CO_{2} laser yielded 6×10^{7} x-ray photons over the full opening angle in a single shot. Single shot x-ray diffraction is performed by passing the x rays though a vertical slit and on to a flat silicon (111 crystal. 10^{2} diffracted photons were detected. The spectrum of the detected x rays is compared to simulation. The diffraction and detection of 10^{2} x rays is a key step to a more efficient time resolved diagnostic in which the number of observed x rays might reach 10^{4}; enabling a unique, flexible x-ray source as a sub-ps resolution diagnostic for studying the evolution of chemical reactions, lattice deformation and melting, and magnetism.

  11. Thin film characterisation by advanced X-ray diffraction techniques

    Energy Technology Data Exchange (ETDEWEB)

    Cappuccio, G.; Terranova, M.L. [eds.] [INFN, Laboratori Nazionali di Frascati, Rome (Italy)

    1996-09-01

    This report described the papers presented at the 5. School on X-ray diffraction from polycrystalline materials held at Frascati (Rome) in 2-5 October 1996. A separate abstract was prepared for each of the papers.

  12. X-ray diffraction radiation in conditions of Cherenkov effect

    NARCIS (Netherlands)

    Tishchenko, A. A.; Potylitsyn, A. P.; Strikhanov, M. N.

    2006-01-01

    X-ray diffraction radiation from ultra-relativistic electrons moving near an absorbing target is considered. The emission yield is found to increase significantly in conditions of Cherenkov effect. (c) 2006 Elsevier B.V. All rights reserved.

  13. A stand-alone mesoporous crystal structure model from in situ X-ray diffraction: nitrogen adsorption on 3D cagelike mesoporous silica SBA-16.

    Science.gov (United States)

    Miyasaka, Keiichi; Hano, Hiroko; Kubota, Yoshiki; Lin, Yangzheng; Ryoo, Ryong; Takata, Masaki; Kitagawa, Susumu; Neimark, Alexander V; Terasaki, Osamu

    2012-08-13

    We present a modeling scheme to analyze cagelike silica mesoporous crystals based on in situ X-ray diffraction (XRD) data collected during gas adsorption-desorption (physisorption) processes. Nitrogen physisorption on a silica mesoporous crystal of SBA-16 was directly monitored by using synchrotron in situ powder XRD measurements conducted at SPring-8. SBA-16 is a well-ordered mesoporous silica in which three-dimensional interconnected cagelike primary mesopores are located at the body-centered cubic lattice points. In addition, the surrounding silica matrix contains random microporous and mesoporous intrawall porosities that are significantly influential to the diffusion properties, and thus important to be quantified for this media. The in situ XRD data exhibits seven Bragg reflections throughout the measurements, and the present method allows one to obtain the maximal and stand-alone information about the pore structure (for example, the mesopore size, the matrix density, the intrawall porosity, and pore surface roughness) together with the nitrogen film evolution in the primary mesopores and the intrawall pore-filling in the silica matrix. We furthermore observe a macroscopic amount of nitrogen adsorbed assuming the density of the fluid, and confirm that the XRD "isotherm" recalculated from the analysis result is consistent with the conventional nitrogen isotherm on a semi-quantitative level; however, these results suggest that the intrawall pores would have a greater contribution to the adsorption than considered based on the conventional isotherm analyses. The present method is readily extendable to any ordered mesopores wrapped by the wall matrix containing a certain intrawall porosity.

  14. Use of X-Ray Diffraction, Molecular Simulations, and Spectroscopy to Determine the Molecular Packing in a Polymer-Fullerene Bimolecular Crystal

    Science.gov (United States)

    2012-09-05

    wileyonlinelibrary.com C O M M U N IC A TIO N Nichole Cates Miller , Eunkyung Cho , Matthias J. N. Junk , Roman Gysel , Chad Risko , Dongwook...of BHJ blends using X-ray diffraction ( XRD ), because the blends were either amorphous or too disordered to yield enough XRD refl ections to...that establishes at the molecular level the properties and function of BHJ solar cells. Specifi cally, we use a combination of XRD techniques

  15. An X-ray diffraction study of titanium oxidation

    Science.gov (United States)

    Wiedemann, K. E.; Unnam, J.

    1984-01-01

    Titanium specimens of commercial purity were exposed at 1100 to 1400 F to laboratory air for times up to 100 hours. The extent of substrate contamination by interstitial oxygen was was determined by a new X-ray diffraction analysis involving transformation of X-ray diffraction intensity bands. The oxygen solid-solubility at the oxide-metal interfaces and its variation with time at temperature were also determined. Diffusion coefficients are deduced from the oxygen depth profiles.

  16. Theory of time-resolved inelastic x-ray diffraction

    DEFF Research Database (Denmark)

    Lorenz, Ulf; Møller, Klaus Braagaard; Henriksen, Niels Engholm

    2010-01-01

    Starting from a general theory of time-resolved x-ray scattering, we derive a convenient expression for the diffraction signal based on a careful analysis of the relevant inelastic scattering processes. We demonstrate that the resulting inelastic limit applies to a wider variety of experimental...... conditions than similar, previously derived formulas, and it directly allows the application of selection rules when interpreting diffraction signals. Furthermore, we present a simple extension to systems simultaneously illuminated by x rays and a laser beam....

  17. X-Ray Diffraction Wafer Mapping Method for Rhombohedral Super-Hetero-Epitaxy

    Science.gov (United States)

    Park, Yoonjoon; Choi, Sang Hyouk; King, Glen C.; Elliott, James R.; Dimarcantonio, Albert L.

    2010-01-01

    A new X-ray diffraction (XRD) method is provided to acquire XY mapping of the distribution of single crystals, poly-crystals, and twin defects across an entire wafer of rhombohedral super-hetero-epitaxial semiconductor material. In one embodiment, the method is performed with a point or line X-ray source with an X-ray incidence angle approximating a normal angle close to 90 deg, and in which the beam mask is preferably replaced with a crossed slit. While the wafer moves in the X and Y direction, a narrowly defined X-ray source illuminates the sample and the diffracted X-ray beam is monitored by the detector at a predefined angle. Preferably, the untilted, asymmetric scans are of {440} peaks, for twin defect characterization.

  18. Ultrafast molecular processes mapped by femtosecond x-ray diffraction

    Science.gov (United States)

    Elsaesser, Thomas

    2012-02-01

    X-ray diffraction with a femtosecond time resolution allows for mapping photoinduced structural dynamics on the length scale of a chemical bond and in the time domain of atomic and molecular motion. In a pump-probe approach, a femtosecond excitation pulse induces structural changes which are probed by diffracting a femtosecond hard x-ray pulse from the excited sample. The transient angular positions and intensities of diffraction peaks give insight into the momentary atomic or molecular positions and into the distribution of electronic charge density. The simultaneous measurement of changes on different diffraction peaks is essential for determining atom positions and charge density maps with high accuracy. Recent progress in the generation of ultrashort hard x-ray pulses (Cu Kα, wavelength λ=0.154 nm) in laser-driven plasma sources has led to the implementation of the powder diffraction and the rotating crystal method with a time resolution of 100 fs. In this contribution, we report new results from powder diffraction studies of molecular materials. A first series of experiments gives evidence of a so far unknown concerted transfer of electrons and protons in ammonium sulfate [(NH4)2SO4], a centrosymmetric structure. Charge transfer from the sulfate groups results in the sub-100 fs generation of a confined electron channel along the c-axis of the unit cell which is stabilized by transferring protons from the adjacent ammonium groups into the channel. Time-dependent charge density maps display a periodic modulation of the channel's charge density by low-frequency lattice motions with a concerted electron and proton motion between the channel and the initial proton binding site. A second study addresses atomic rearrangements and charge dislocations in the non-centrosymmetric potassium dihydrogen phosphate [KH2PO4, KDP]. Photoexcitation generates coherent low-frequency motions along the LO and TO phonon coordinates, leaving the average atomic positions unchanged

  19. 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.

  20. Nanosecond x-ray Laue diffraction apparatus suitable for laser shock compression experiments.

    Science.gov (United States)

    Suggit, Matthew; Kimminau, Giles; Hawreliak, James; Remington, Bruce; Park, Nigel; Wark, Justin

    2010-08-01

    We have used nanosecond bursts of x-rays emitted from a laser-produced plasma, comprised of a mixture of mid-Z elements, to produce a quasiwhite-light spectrum suitable for performing Laue diffraction from single crystals. The laser-produced plasma emits x-rays ranging in energy from 3 to in excess of 10 keV, and is sufficiently bright for single shot nanosecond diffraction patterns to be recorded. The geometry is suitable for the study of laser-shocked crystals, and single-shot diffraction patterns from both unshocked and shocked silicon crystals are presented.

  1. 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.

  2. 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.

  3. X-ray characterization by energy-resolved powder diffraction

    Directory of Open Access Journals (Sweden)

    G. Cheung

    2016-08-01

    Full Text Available A method for single-shot, nondestructive characterization of broadband x-ray beams, based on energy-resolved powder diffraction, is described. Monte-Carlo simulations are used to simulate data for x-ray beams in the keV range with parameters similar to those generated by betatron oscillations in a laser-driven plasma accelerator. The retrieved x-ray spectra are found to be in excellent agreement with those of the input beams for realistic numbers of incident photons. It is demonstrated that the angular divergence of the x rays can be deduced from the deviation of the detected photons from the Debye-Scherrer rings which would be produced by a parallel beam. It is shown that the angular divergence can be measured as a function of the photon energy, yielding the angularly resolved spectrum of the input x-ray beam.

  4. The diffraction of X-rays by close-packed polytypic crystals containing single stacking faults. Pt. 3. Measurements of diffraction effects caused by stacking faults in plate or film form samples

    Energy Technology Data Exchange (ETDEWEB)

    Michalski, E. [Military Acad. of Technol., Warsaw (Poland). Inst. of Tech. Phys.; Piecek, W. [Military Acad. of Technol., Warsaw (Poland). Inst. of Tech. Phys.; Demianiuk, M. [Military Acad. of Technol., Warsaw (Poland). Inst. of Tech. Phys.

    1995-07-01

    A theory that describes the diffraction effects from stacking faults in close-packed polytypic crystal structures was developed in two previous papers of this series. In this paper, attention is paid to the measurement of these diffraction effects for the cases where needle-shaped or rod-like specimens cannot be made from the given sample (e.g. thin films) or when single-crystal samples should not be destroyed for preparing such specimens. For this purpose, methods of measurement based on standard X-ray diffraction equipment such as oscillation or Weissenberg cameras and a powder diffraction diffractometer have been developed A complete description of the limitation of the area of the reciprocal lattice that can intersect the Ewald sphere has been provided. Examples of the results obtained by these methods are given. The diffractometer two-dimensional scanning method, which allows an undistorted reciprocal lattice to be recorded and higher precision and results more convenient for mathematical treatment than in photographic methods to be obtained, seems to be especially interesting. (orig.).

  5. Ultrafast structural dynamics studied by kilohertz time-resolved x-ray diffraction

    Institute of Scientific and Technical Information of China (English)

    郭鑫; 江舟亚; 陈龙; 陈黎明; 辛建国; 陈洁

    2015-01-01

    Ultrashort multi-keV x-ray pulses are generated by electron plasma produced by the irradiation of femtosecond pulses on metals. These sub-picosecond x-ray pulses have extended the field of x-ray spectroscopy into the femtosecond time domain. However, pulse-to-pulse instability and long data acquisition time restrict the application of ultrashort x-ray systems operating at low repetition rates. Here we report on the performance of a femtosecond laser plasma-induced hard x-ray source that operates at 1-kHz repetition rate, and provides a flux of 2.0 × 1010 photons/s of Cu Kα radiation. Using this system for time-resolved x-ray diffraction experiments, we record in real time, the transient processes and structural changes induced by the interaction of 400-nm femtosecond pulse with the surface of a 200-nm thick Au (111) single crystal.

  6. Table of interplanar spacings for crystal-structure determinations by X-ray diffraction with molybdenum, copper, cobalt, iron, and chromium radiations

    Science.gov (United States)

    Kittel, J Howard

    1945-01-01

    For a simple diffraction pattern, the time required to calculate interplanar distances from measurements of the pattern is not excessive. If more than a few lines are present, however, or if several patterns are to be studied, it is very advantageous to have available a table giving interplanar spacings directly in terms of the linear measurements made on the film of the lines appearing on the diffraction pattern. The preparation of the table given here was undertaken when the expansion of research activities involving X-ray diffraction techniques indicated that such a table would greatly decrease the time required to analyze diffraction patterns. The table was prepared for use with K alpha(sub 1) radiation from the following target materials: molybdenum, copper, cobalt, iron, and chromium.

  7. Thermal Equation of State of Fe7C3 by Single Crystal X-ray Diffraction with Implications for Carbon in the Inner Core

    Science.gov (United States)

    Lai, X.; Chen, B.; Zhu, F.; Liu, J.; Hu, Y.; Dera, P.; Zhang, D.

    2016-12-01

    Carbon is one of the principle candidates for the light elements in Earth's core partly due to its high cosmic abundance and high solubility in Fe-Ni alloy [1,2]. Its alloys with iron (Fe), iron carbides, are also found in reducing environment in the Earth's mantle [3]. Eckstrom-Adcock carbide Fe7C3 is likely to be the first phase to solidify from Fe-C melt under core conditions, and has thus been proposed to be an inner core candidate [4]. The crystal structure of Fe7C3, however, remains controversial and its thermoelastic properties, crucial for extrapolating the room-temperature mineral physics data to high temperature conditions, were rarely investigated approaching core pressures. In this study, we performed synchrotron single-crystal X-ray diffraction (XRD) measurements using externally-heated diamond anvil cells and determined the crystal structure, lattice parameters and atomic positions of Fe7C3 up to 75 GPa and 800 K. The ambient pressure unit cell volume (V0), bulk modulus (K0) and its first derivative (K0') at 300 K were determined by fitting the third-order Birch-Murnaghan equation of state. The pressure-volume-temperature data set for Fe7C3 could be well represented by a Mie-Grüneisen-Debye thermal equation of state. We found that the c/a ratio of Fe7C3 decreases continuously up to 45 GPa and increases abruptly at around 55 GPa at 300K, probably due to the high-spin to low-spin transition. The thermal expansion of c axis is notably larger than other axes. The determined thermoelastic property of Fe7C3 will permit stringent test of a Fe-C inner core compositional model. References: [1] Wood, Bernard J. Earth Planet. Sci. Lett. 117.3 (1993): 593-607. [2] Wood, Bernard J., Jie Li, and Anat Shahar. Rev. Mineral. Geochem. 75 (2013): 231-250. [3] Kaminsky, Felix V., and Richard Wirth. Can. Mineral. 49.2 (2011): 555-572. [4] Fei, Yingwei, and Eli Brosh. Earth Planet. Sci. Lett. 408 (2014): 155-162.

  8. In situ X-ray diffraction during pulsed laser deposition

    Energy Technology Data Exchange (ETDEWEB)

    Vonk, Vedran [Max-Planck-Institute for Metals Research, Stuttgart (Germany); Huijben, Mark [University of California, Berkeley (United States); Driessen, Kurt; Rijnders, Guus; Blank, Dave; Harkema, Sybolt [University of Twente, Enschede (Netherlands); Graafsma, Heinz [Deutsches Elektronen- Synchrotron, Hamburg (Germany)

    2007-07-01

    The use of in situ X-ray diffraction for the study of thin film growth enables in a straightforward way to derive the atomic structure, because the kinematical scattering approximation holds. Here we present the results of studying the heteroepitaxial growth by Pulsed Laser Deposition of complex oxides such as the High-T c superconductor YBa{sub 2}Cu{sub 3}O{sub 7-x} and the insulator LaAlO{sub 3} on SrTiO{sub 3}(001) substrates. A special sample chamber has been constructed to be used with synchrotron X-rays. Detailed pictures of the growth kinetics and of the atomic interface structure at deposition conditions result from fitting quantitatively both the intensity growth oscillations and the crystal truncation rods. The growth of the complex oxide thin films presented here is characterized by substantial interlayer-mass transport and large deviations from the bulk room-temperature atomic structure. The results show the effects of the interplay between formation and diffusion energies on the processes of nucleation and kinetics during heteroepitaxial growth.

  9. Enhancement of coherent X-ray diffraction from nanocrystals by introduction of X-ray optics.

    Science.gov (United States)

    Robinson, Ian; Pfeiffer, Franz; Vartanyants, Ivan; Sun, Yugang; Xia, Younan

    2003-09-22

    Coherent X-ray Diffraction is applied to investigate the structure of individual nanocrystalline silver particles in the 100nm size range. In order to enhance the available signal, Kirkpatrick-Baez focusing optics have been introduced in the 34-ID-C beamline at APS. Concerns about the preservation of coherence under these circumstances are addressed through experiment and by calculations.

  10. Comparison between Double Crystals X-ray Diffraction and Micro-Raman Measurement on Composition Determination of High Ge Content Si1-xGex Layer Epitaxied on Si Substrate

    Institute of Scientific and Technical Information of China (English)

    Lei ZHAO; Yuhua ZUO; Buwen CHENG; Jinzhong YU; Qiming WANG

    2006-01-01

    It is important to acquire the composition of Si1-xGex layer, especially that with high Ge content, epitaxied on Si substrate. Two nondestructive examination methods, double crystals X-ray diffraction(DCXRD)and micro-Raman measurement, were introduced comparatively to determine x value in Si1-xGex layer, which show that while the two methods are consistent with each other when x is low, the results obtained from double crystals X-ray diffraction are not credible due to the large strain relaxation occurring in Si1-xGex layers when Ge content is higher than about 20%. Micro-Raman measurement is more appropriate for determining high Ge content than DCXRD.

  11. Spectroscopic imaging, diffraction, and holography with x-ray photoemission

    Energy Technology Data Exchange (ETDEWEB)

    1992-02-01

    X-ray probes are capable of determining the spatial structure of an atom in a specific chemical state, over length scales from about a micron all the way down to atomic resolution. Examples of these probes include photoemission microscopy, energy-dependent photoemission diffraction, photoelectron holography, and X-ray absorption microspectroscopy. Although the method of image formation, chemical-state sensitivity, and length scales can be very different, these X-ray techniques share a common goal of combining a capability for structure determination with chemical-state specificity. This workshop will address recent advances in holographic, diffraction, and direct imaging techniques using X-ray photoemission on both theoretical and experimental fronts. A particular emphasis will be on novel structure determinations with atomic resolution using photoelectrons.

  12. Chemistry of Metal-organic Frameworks Monitored by Advanced X-ray Diffraction and Scattering Techniques.

    Science.gov (United States)

    Mazaj, Matjaž; Kaučič, Venčeslav; Zabukovec Logar, Nataša

    2016-01-01

    The research on metal-organic frameworks (MOFs) experienced rapid progress in recent years due to their structure diversity and wide range of application opportunities. Continuous progress of X-ray and neutron diffraction methods enables more and more detailed insight into MOF's structural features and significantly contributes to the understanding of their chemistry. Improved instrumentation and data processing in high-resolution X-ray diffraction methods enables the determination of new complex MOF crystal structures in powdered form. By the use of neutron diffraction techniques, a lot of knowledge about the interaction of guest molecules with crystalline framework has been gained in the past few years. Moreover, in-situ time-resolved studies by various diffraction and scattering techniques provided comprehensive information about crystallization kinetics, crystal growth mechanism and structural dynamics triggered by external physical or chemical stimuli. The review emphasizes most relevant advanced structural studies of MOFs based on powder X-ray and neutron scattering.

  13. 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.

  14. Glancing angle x-ray diffraction : A different approach

    NARCIS (Netherlands)

    Brussel, B.A. van; Hosson, J.Th.M. De

    1994-01-01

    This letter describes a novel technique of diffracted beam glancing angle x-ray diffraction by which depth profiles of stresses and transformed phases in structures like implanted materials can be determined. An important feature is that this method may be applied successfully in a standard powder d

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. Dynamical x-ray diffraction from an icosahedral Al-Pd-Mn quasicrystal

    Energy Technology Data Exchange (ETDEWEB)

    Kycia, S.

    1996-04-23

    Primary extinction effects in diffraction from single grains of Al-Pd- Mn, and presumably many other FCI alloys, may be significant and should be corrected for prior to use of diffraction data in structural determinations. Probes based on dynamical diffraction effects, such as x-ray standing wave fluorescence, multiple beam interference, and x-ray transmission topographs, may now be used to study the bulk and surface structure of some quasicrystals. The observation of dynamical diffraction from icosahedral Al-Pd-Mn is a striking confirmation of the fact that quasicrystals can present a degree of structural perfection comparable to that found in the best periodic intermetallic crystals.

  20. 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

  1. 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.

  2. Solvent exchange in a metal–organic framework single crystal monitored by dynamic in situ X-ray diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Cox, Jordan M.; Walton, Ian M.; Bateman, Gage; Benson, Cassidy A.; Mitchell, Travis; Sylvester, Eric; Chen, Yu-Sheng; Benedict, Jason B.

    2017-07-25

    Understanding the processes by which porous solid-state materials adsorb and release guest molecules would represent a significant step towards developing rational design principles for functional porous materials. To elucidate the process of liquid exchange in these materials, dynamicin situX-ray diffraction techniques have been developed which utilize liquid-phase chemical stimuli. Using these time-resolved diffraction techniques, the ethanol solvation process in a flexible metal–organic framework [Co(AIP)(bpy)0.5(H2O)]·2H2O was examined. The measurements provide important insight into the nature of the chemical transformation in this system including the presence of a previously unreported neat ethanol solvate structure.

  3. On the P-induced behavior of the zeolite phillipsite: an in situ single-crystal synchrotron X-ray diffraction study

    Science.gov (United States)

    Comboni, Davide; Gatta, G. Diego; Lotti, Paolo; Merlini, Marco; Liermann, Hanns-Peter

    2017-01-01

    The elastic behavior and the structural evolution at high pressure of a natural phillipsite have been investigated by in situ single-crystal X-ray diffraction up to 9.44 GPa, using a diamond anvil cell and the nominally penetrating P-transmitting fluid methanol:ethanol:water (16:3:1) mix. Although no phase transition was observed within the P-range investigated, two different compressional regimes occur. Between 0.0001 and 2.0 GPa, the refined elastic parameters, calculated by a second-order Birch-Murnaghan equation of state (BM-EoS) fit, are V 0 = 1005(1) Å3, K 0 = 89(8) GPa for the unit-cell volume; a 0 = 9.914(7) Å, K a = 81(12) GPa for the a-axis; b 0 = 14.201(9) Å, K b = 50(5) GPa for the b-axis; and c 0 = 8.707(2) Å, K c = 107(8) GPa for the c-axis ( K a : K b : K c 1.62:1:2.14). Between 2.0 and 9.4 GPa, a P-induced change in the configuration of H2O molecules, coupled with a change in the tilting mechanisms of the framework tetrahedra, gives rise to a second compressional regime, in which the phillipsite structure is softer if compared to the first compressional range. In the second compressional regime, the refined elastic parameters, calculated by a second-order BM-EoS fit, are V 0 = 1098 (7) Å3, K 0 = 18.8(7) GPa for the unit-cell volume; a 0 = 10.07(3) Å, K a = 30(2) GPa for the a-axis; b 0 = 14.8(1) Å, K b = 11(1) GPa for the b-axis; and c 0 = 8.94(2) Å, K c = 21(1) GPa for the c-axis ( K a : K b : K c 2.72:1:1.90). The evolution of the monoclinic β angle with pressure shows two distinct trends in the two compressional regimes: with a negative slope between 0.0001 and 2.0 GPa, and a positive slope between 2.0 and 9.4 GPa. The mechanisms, at the atomic scale, that govern the two compressional regimes of the phillipsite structure are described.

  4. X-Ray-Diffraction Tests Of Irradiated Electronic Devices: I

    Science.gov (United States)

    Shaw, David C.; Lowry, Lynn E.; Barnes, Charles E.

    1993-01-01

    X-ray-diffraction tests performed on aluminum conductors in commercial HI1-507A complementary metal oxide/semiconductor (CMOS) integrated-circuit analog multiplexers, both before and after circuits exposed to ionizing radiation from Co(60) source, and after postirradiation annealing at ambient and elevated temperatures. Tests in addition to electrical tests performed to determine effects of irradiation and of postirradiation annealing on electrical operating characteristics of circuits. Investigators sought to determine whether relationship between effects of irradiation on devices and physical stresses within devices. X-ray diffraction potentially useful for nondestructive measurement of stresses.

  5. A single crystal X-ray and powder neutron diffraction study on NASICON-type Li1+xAlxTi2-x(PO4)3 (0 ≤ x ≤ 0.5) crystals: Implications on ionic conductivity

    Science.gov (United States)

    Redhammer, G. J.; Rettenwander, D.; Pristat, S.; Dashjav, E.; Kumar, C. M. N.; Topa, D.; Tietz, F.

    2016-10-01

    Single crystals of NASICON-type material Li1+xTi2-xAlx(PO4)3 (LATP) with 0 ≤ x ≤ 0.5 were successfully grown using long-term sintering techniques. Sample material was studied by chemical analysis, single crystal X-ray and neutron diffraction. The Ti4+ replacement scales very well with the Al3+ and Li+ incorporation. The additional Li+ thereby enters the M3 cavity of the NASICON framework at x, y, z ∼ (0.07, 0.34, 0.09) and is regarded to be responsible for the enhanced Li+ conduction of LATP as compared to Al-free LTP. Variations in structural parameters, associated with the Ti4+ substitution with Al3+ + Li+ will be discussed in detail in this paper.

  6. Crystallization and preliminary X-ray diffraction analyses of pseudechetoxin and pseudecin, two snake-venom cysteine-rich secretory proteins that target cyclic nucleotide-gated ion channels

    Energy Technology Data Exchange (ETDEWEB)

    Suzuki, Nobuhiro [Institute of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8572 (Japan); Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602 (Japan); Yamazaki, Yasuo [Department of Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588 (Japan); Fujimoto, Zui [Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602 (Japan); Morita, Takashi [Department of Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588 (Japan); Mizuno, Hiroshi, E-mail: mizuno-hiroshi@aist.go.jp [Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602 (Japan); VALWAY Technology Center, NEC Soft Ltd, Koto-ku, Tokyo 136-8627 (Japan); Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, Central 6, Tsukuba, Ibaraki 305-8566 (Japan); Institute of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8572 (Japan)

    2005-08-01

    Crystals of pseudechetoxin and pseudecin, potent peptidic inhibitors of cyclic nucleotide-gated ion channels, have been prepared and X-ray diffraction data have been collected to 2.25 and 1.90 Å resolution, respectively. Cyclic nucleotide-gated (CNG) ion channels play pivotal roles in sensory transduction of retinal and olfactory neurons. The elapid snake toxins pseudechetoxin (PsTx) and pseudecin (Pdc) are the only known protein blockers of CNG channels. These toxins are structurally classified as cysteine-rich secretory proteins and exhibit structural features that are quite distinct from those of other known small peptidic channel blockers. This article describes the crystallization and preliminary X-ray diffraction analyses of these toxins. Crystals of PsTx belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 60.30, b = 61.59, c = 251.69 Å, and diffraction data were collected to 2.25 Å resolution. Crystals of Pdc also belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with similar unit-cell parameters a = 60.71, b = 61.67, c = 251.22 Å, and diffraction data were collected to 1.90 Å resolution.

  7. Single-Crystal X-Ray Diffraction of Orthoenstatite to 48 GPa: New High-Pressure Phases with 4-, 5-, and 6-Coordinated Silicon

    Science.gov (United States)

    Finkelstein, G. J.; Dera, P. K.; Duffy, T. S.

    2013-12-01

    Orthopyroxene (opx, (Mg,Fe)SiO3) is one of the major phases in Earth's upper mantle, comprising ~20% of the region by volume. At high pressures and temperatures, this phase undergoes several well-characterized phase transitions. Its behavior at low temperature is less well known, but may be important for cold subducting slabs (1, 2). Previous studies (3, 4) reported that MgSiO3 orthoenstatite persists up to ~12 GPa, and a phase transition above this pressure was recently discovered by Zhang et al. (5). This structure, which we call β-opx (designated HPCEN2 in previous studies), is related to one predicted by theory (6), and has P21/c monoclinic symmetry. It retains an opx topology despite its lower symmetry, distinguishing it from a true clinopyroxene. We conducted single-crystal X-ray diffraction experiments in a diamond anvil cell at GSECARS and HPCAT at the APS. Mg0.91Fe0.09SiO3 orthopyroxene was compressed in a neon pressure medium with a gold pressure standard. In addition to the orthopyroxene to β-opx transition, we observe two further phase changes at ~28 GPa and ~38 GPa. The transitions result in volume reductions of ~2.5% and ~3.9%, respectively. The Si layers in both new structures are intermediate between the opx structure and that of the ilmenite-structured akimotoite polymorph. Akimotoite consists of edge-sharing MgO6 and SiO6 octahedra arranged in alternating honeycomb sheets. A theoretical study suggested clinoenstatite could transform directly to akimotoite at low temperatures through a shear-based mechanism (7). Here, we observe that the path toward akimotoite-like Si layers is stepwise. In the new MgSiO3 structures, the initial chains of SiO4 tetrahedra are partially converted to the characteristic 6-coordinated honeycomb layers. This results in some 5-coordinated Si sites in both structures. Due to the increased coordination number, we are calling the new structures α- and β-post-orthopyroxene (α-popx and β-popx). The Mg layers, however, do

  8. 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...

  9. Apparatus for use in examining the lattice of a semiconductor wafer by X-ray diffraction

    Science.gov (United States)

    Parker, D. L.; Porter, W. A. (Inventor)

    1978-01-01

    An improved apparatus for examining the crystal lattice of a semiconductor wafer utilizing X-ray diffraction techniques was presented. The apparatus is employed in a method which includes the step of recording the image of a wafer supported in a bent configuration conforming to a compound curve, produced through the use of a vacuum chuck provided for an X-ray camera. The entire surface thereof is illuminated simultaneously by a beam of incident X-rays which are projected from a distant point-source and satisfy conditions of the Bragg Law for all points on the surface of the water.

  10. Increasing the X-ray Diffraction Power of Protein Crystals by Dehydration: The Case of Bovine Serum Albumin and a Survey of Literature Data

    Directory of Open Access Journals (Sweden)

    Irene Russo Krauss

    2012-03-01

    Full Text Available Serum albumin is one of the most widely studied proteins. It is the most abundant protein in plasma with a typical concentration of 5 g/100 mL and the principal transporter of fatty acids in plasma. While the crystal structures of human serum albumin (HSA free and in complex with fatty acids, hemin, and local anesthetics have been characterized, no crystallographic models are available on bovine serum albumin (BSA, presumably because of the poor diffraction power of existing hexagonal BSA crystals. Here, the crystallization and diffraction data of a new BSA crystal form, obtained by the hanging drop method using MPEG 5K as precipitating agent, are presented. The crystals belong to space group C2, with unit-cell parameters a = 216.45 Å, b = 44.72 Å, c = 140.18 Å, β = 114.5°. Dehydration was found to increase the diffraction limit of BSA crystals from ~8 Å to 3.2 Å, probably by improving the packing of protein molecules in the crystal lattice. These results, together with a survey of more than 60 successful cases of protein crystal dehydration, confirm that it can be a useful procedure to be used in initial screening as a method of improving the diffraction limits of existing crystals.

  11. Electrochemical cell for in situ x-ray diffraction under ultrapure conditions

    DEFF Research Database (Denmark)

    Koop, T.; Schindler, W.; Kazimirov, A.

    1998-01-01

    An electrochemical cell has been developed for in situ x-ray diffraction from a working electrode under clean conditions equivalent to ultrahigh vacuum conditions of 5 x 10(-10) mbar. The substrate crystals can be prepared ex situ and transferred into the cell under protection of ultrapure water...... of the crystal using a Luggin capillary and a standard reference electrode. We demonstrate the performance of our cell by in situ synchrotron x-ray diffraction measurements on ultrathin Co layers electrodeposited on Cu(001) in an aqueous H(2)SO(4)/CoSO(4) solution. (C) 1998 American Institute of Physics....

  12. X-ray diffraction at Matter in Extreme Conditions endstation

    Science.gov (United States)

    Xing, Zhou; Galtier, Eric; Lee, Hae Ja; Nagler, Bob

    2015-11-01

    Understanding dynamic response at the atomic level under extreme conditions is highly sought after goal to science frontiers studying warm dense matter, high pressure, geoscience, astrophysics, and planetary science. Thus it is of importance to determine the high pressure phases or metastable phases of material under shock compression. In situ X-ray diffraction technique using LCLS free electron laser X-ray is a powerful tool to record structural behavior and microstructure evolution in dense matter. Shock-induced compression and phase transitions of material lead to changes of the lattice spacing or evolution of new X-ray diffraction patterns. In this talk, we describe a platform dedicated for the X-ray diffraction studies at Matter in Extreme Conditions (MEC), which can be used to reconstruct a complete diffraction pattern from numerous detectors, optimize detector positioning in a timely manner, extract the lattice spacing profiles and texture features. This platform is available to the user community for real-time analysis. We will also discuss experimental results, using this platform, on the crystalline silicon phase transitions up to 60 GPa.

  13. X-Ray Diffraction Simulation Using Laser Pointers and Printers.

    Science.gov (United States)

    Johnson, Neil E.

    2001-01-01

    Uses a laser pointer to demonstrate the analogy between optical and X-ray diffraction and a laser printer with 600 or 1200 dot resolution to create and modify arrays, print them on transparencies, and illuminate them with laser pointers. Includes 14 references. (Author/YDS)

  14. X-Ray Diffraction Simulation Using Laser Pointers and Printers.

    Science.gov (United States)

    Johnson, Neil E.

    2001-01-01

    Uses a laser pointer to demonstrate the analogy between optical and X-ray diffraction and a laser printer with 600 or 1200 dot resolution to create and modify arrays, print them on transparencies, and illuminate them with laser pointers. Includes 14 references. (Author/YDS)

  15. Powder X-ray diffraction study af alkali alanates

    DEFF Research Database (Denmark)

    Cao, Thao; Mosegaard Arnbjerg, Lene; Jensen, Torben René

    Powder X-ray diffraction study of alkali alanates Thao Cao, Lene Arnbjerg, Torben R. Jensen. Center for Materials Crystallography (CMC), Center for Energy Materials (CEM), iNANO and Department of Chemistry, Aarhus University, DK-8000, Denmark. Abstract: To meet the energy demand in the future...

  16. X-Ray diffraction Investigation of Electrochemically Deposited Copper

    DEFF Research Database (Denmark)

    Pantleon, Karen; Jensen, Jens Dahl; Somers, Marcel A.J.

    2004-01-01

    by the determination of X-ray diffraction (XRD) pole figures and the calculation of the orientation distribution functions. XRD results are discussed in relation to the morphologies of the electrodeposits as investigated with light optical microscopy and correlated with the process parameters during electrodeposition....

  17. The three dimensional X-ray diffraction technique

    DEFF Research Database (Denmark)

    Juul Jensen, Dorte; Poulsen, Henning Friis

    2012-01-01

    This introductory tutorial describes the so called 3 dimensional X-ray diffraction (3DXRD) technique, which allows bulk non-destructive structural characterizations of crystalline materials. The motivations and history behind the development of this technique are described and its potentials...

  18. Computer Simulation and X-ray Diffraction of Nanocrystals

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    X-ray diffraction of structure in nanocrystalline α-Fe and Cu was studied by atomistic simulation. Atomic position equilibrium was reached by using molecular dynamics method to simulate nanocrystalline structure with Finnis potentials to model interatomic interactions. lt was found that the boundary component exhibits short-range order, and the distortion in crystalline component increases with the decrease of grain size.

  19. Incommensurate density modulation in a Na-rich plagioclase feldspar: Z-contrast imaging and single-crystal X-ray diffraction study.

    Science.gov (United States)

    Xu, Huifang; Jin, Shiyun; Noll, Bruce C

    2016-12-01

    Plagioclase feldspars are the most abundant mineral in the Earth's crust. Intermediate plagioclase feldspars commonly display incommensurately modulated or aperiodic structures. Z-contrast images show both Ca-Na ordering and density modulation. The local structure of lamellae domains has I1-like symmetry. The neighboring lamellae domains are in an inversion twinning relationship. With a state-of-the-art X-ray diffraction unit, second-order satellite reflections (f-reflections) are observed for the first time in andesine (An45), a Na-rich e-plagioclase. The f-reflections indicate a structure with a density modulation which is close to a Ca-rich e-plagioclase. The similarity between this e-andesine structure and previously solved e-labradorite structure is confirmed. Refinement of the structure shows density modulation of ∼ 7 mol % in compositional variation of the anorthite (An) component. The results from Z-contrast imaging and low-temperature single X-ray diffraction (XRD) provide a structure consistent with density modulation. The discovery of f-reflections in Na-rich e-plagioclase extends the composition range of e1 structure with density modulation to as low as at least An45, which is the lower end of the composition range of Bøggild intergrowth. The new result supports the loop-shaped solvus for Bøggild intergrowth, below which is a homogenous stable area for e1 structure in the phase diagram. The phase transition between e2 structure without density modulation and e1 structure with density modulation should happen at low temperature. There is a change in modulation period accompanying the phase transition, as well as higher occupancy of Al in the T1o site. The andesine with density modulation also indicates extremely slow cooling of its host rock.

  20. A cooled avalanche photodiode detector for X-ray magnetic diffraction experiments

    CERN Document Server

    Kishimoto, S; Ito, M

    2001-01-01

    A cooled avalanche photodiode (APD) detector was developed for X-ray magnetic diffraction experiments. A stack of four silicon APDs was cooled down to 243 K by a thermoelectric cooler. The energy widths of 0.89 and 1.55 keV (FWHM) were obtained for 8.05 keV X-rays at 1x10 sup 6 s sup - sup 1 and for 16.53 keV X-rays at 2x10 sup 6 s sup - sup 1 , respectively. Test measurements of X-ray magnetic diffraction were executed using a terbium single crystal and white synchrotron radiation. A peak width of (1 0 3) reflection (5.4 keV) was roughly three times wider than that with a high-purity germanium detector.

  1. Computing Composition/Depth Profiles From X-Ray Diffraction

    Science.gov (United States)

    Wiedemann, K. E.; Unnam, J.

    1986-01-01

    Diffraction-intensity bands deconvolved relatively quickly. TIBAC constructs composition/depth profiles from X-ray diffraction-intensity bands. Intensity band extremely sensitive to shape of composition/depth profile. TIBAC incorporates straightforward transformation of intensity band that retains accuracy of earlier simulation models, but is several orders of magnitude faster in total computational time. TIBAC written in FORTRAN 77 for batch execution.

  2. Amorphous silica studied by high energy x-ray diffraction

    DEFF Research Database (Denmark)

    Poulsen, H.F.; Neuefeind, J.; Neumann, H.B.

    1995-01-01

    The use of hard X-rays (60-300 keV) for diffraction studies of disordered materials has several advantages: higher resolution in direct space, smaller correction terms, removal of truncation effects, the possibility for operating in extreme environments and for direct comparison between X-ray.......3(3)degrees with a rms value of 4.2(3)degrees. For the Si-O-Si bond angle, several types of distribution V(alpha) = V-1(alpha) sin(alpha) were investigated. Best fits were obtained for rather broad distributions with V having its maximum at 147 degrees and V-1 at 180 degrees....

  3. Diffraction enhanced X-ray imaging of mammals crystalline lens

    Energy Technology Data Exchange (ETDEWEB)

    Antunes, A. [Departamento de Fisica Aplicada, USP, CP 66318, 05315-970 Sao Paulo, SP (Brazil)]. E-mail: antunes@if.usp.br; Hoennicke, M.G. [LORXI, Departamento de Fisica, Universidade Federal do Parana, Curitiba (Brazil); Safatle, A.M.V. [Faculdade de Medicina Veterinaria e Zootecnia, USP, 05508-900 Sao Paulo, SP (Brazil); Cusatis, C. [LORXI, Departamento de Fisica, Universidade Federal do Parana, Curitiba (Brazil); Moraes Barros, P.S. [Faculdade de Medicina Veterinaria e Zootecnia, USP, 05508-900 Sao Paulo, SP (Brazil); Morelhao, S.L. [Departamento de Fisica Aplicada, USP, CP 66318, 05315-970 Sao Paulo, SP (Brazil)

    2005-08-15

    Crystalline lenses are transparent biological materials where the organization of the lens fibers can also be affected by changes at molecular level, and therefore the structure and morphology of the tissue can be correlated to the loss of transparency of the lens. In this work, internal structure of mammal lenses regarding the long-range ordering of the fibers are investigated by diffraction enhanced X-ray imaging (DEI) radiography. Moreover, DEI and absorption X-ray synchrotron radiographs for healthy and cataractous crystalline lenses are compared. Significant differences in healthy and cataractous crystalline lenses are observed.

  4. Purification, crystallization and preliminary X-ray diffraction of wild-type and mutant recombinant human transforming growth factor beta-induced protein (TGFBIp).

    Science.gov (United States)

    Runager, Kasper; García-Castellanos, Raquel; Valnickova, Zuzana; Kristensen, Torsten; Nielsen, Niels Chr; Klintworth, Gordon K; Gomis-Rüth, F Xavier; Enghild, Jan J

    2009-03-01

    Transforming growth factor beta-induced protein (TGFBIp) has been linked to several corneal dystrophies as certain point mutations in the protein may give rise to a progressive accumulation of insoluble protein material in the human cornea. Little is known about the biological functions of this extracellular protein, which is expressed in various tissues throughout the human body. However, it has been found to interact with a number of extracellular matrix macromolecules such as collagens and proteoglycans. Structural information about TGFBIp might prove to be a valuable tool in the elucidation of its function and its role in corneal dystrophies caused by mutations in the TGFBI gene. A simple method for the purification of wild-type and mutant forms of recombinant human TGFBIp from human cells under native conditions is presented here. Moreover, the crystallization and preliminary X-ray analysis of TGFBIp are reported.

  5. MSL Chemistry and Mineralogy X-Ray Diffraction X-Ray Fluorescence (CheMin) Instrument

    Science.gov (United States)

    Zimmerman, Wayne; Blake, Dave; Harris, William; Morookian, John Michael; Randall, Dave; Reder, Leonard J.; Sarrazin, Phillipe

    2013-01-01

    This paper provides an overview of the Mars Science Laboratory (MSL) Chemistry and Mineralogy Xray Diffraction (XRD), X-ray Fluorescence (XRF) (CheMin) Instrument, an element of the landed Curiosity rover payload, which landed on Mars in August of 2012. The scientific goal of the MSL mission is to explore and quantitatively assess regions in Gale Crater as a potential habitat for life - past or present. The CheMin instrument will receive Martian rock and soil samples from the MSL Sample Acquisition/Sample Processing and Handling (SA/SPaH) system, and process it utilizing X-Ray spectroscopy methods to determine mineral composition. The Chemin instrument will analyze Martian soil and rocks to enable scientists to investigate geophysical processes occurring on Mars. The CheMin science objectives and proposed surface operations are described along with the CheMin hardware with an emphasis on the system engineering challenges associated with developing such a complex instrument.

  6. MSL Chemistry and Mineralogy X-Ray Diffraction X-Ray Fluorescence (CheMin) Instrument

    Science.gov (United States)

    Zimmerman, Wayne; Blake, Dave; Harris, William; Morookian, John Michael; Randall, Dave; Reder, Leonard J.; Sarrazin, Phillipe

    2013-01-01

    This paper provides an overview of the Mars Science Laboratory (MSL) Chemistry and Mineralogy Xray Diffraction (XRD), X-ray Fluorescence (XRF) (CheMin) Instrument, an element of the landed Curiosity rover payload, which landed on Mars in August of 2012. The scientific goal of the MSL mission is to explore and quantitatively assess regions in Gale Crater as a potential habitat for life - past or present. The CheMin instrument will receive Martian rock and soil samples from the MSL Sample Acquisition/Sample Processing and Handling (SA/SPaH) system, and process it utilizing X-Ray spectroscopy methods to determine mineral composition. The Chemin instrument will analyze Martian soil and rocks to enable scientists to investigate geophysical processes occurring on Mars. The CheMin science objectives and proposed surface operations are described along with the CheMin hardware with an emphasis on the system engineering challenges associated with developing such a complex instrument.

  7. Crystallization and preliminary X-ray diffraction studies of tetrameric malate dehydrogenase from the novel Antarctic psychrophile Flavobacterium frigidimaris KUC-1

    Energy Technology Data Exchange (ETDEWEB)

    Fujii, Tomomi [Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011 (Japan); Oikawa, Tadao; Muraoka, Ikuo [Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, Suita, Osaka 564-8680 (Japan); Soda, Kenji [Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011 (Japan); Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, Suita, Osaka 564-8680 (Japan); Hata, Yasuo, E-mail: hata@scl.kyoto-u.ac.jp [Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011 (Japan)

    2007-11-01

    A psychrophilic malate dehydrogenase from the novel Antarctic bacterium F. frigidimaris KUC-1 was crystallized using the hanging-drop vapour-diffusion method. The crystals contained one tetrameric molecule per asymmetric unit. The best crystal diffracted to 1.8 Å resolution. Flavobacterium frigidimaris KUC-1 is a novel psychrotolerant bacterium isolated from Antarctic seawater. Malate dehydrogenase (MDH) is an essential metabolic enzyme in the citric acid cycle and has been cloned, overexpressed and purified from F. frigidimaris KUC-1. In contrast to the already known dimeric form of MDH from the psychrophile Aquaspirillium arcticum, F. frigidimaris MDH exists as a tetramer. It was crystallized at 288 K by the hanging-drop vapour-diffusion method using ammonium sulfate as the precipitating agent. The crystal diffracted to a maximum resolution of 1.80 Å. It contains one tetrameric molecule in the asymmetric unit.

  8. X-ray magnetic diffraction of ferromagnets with synchrotron radiation

    CERN Document Server

    Ito, M

    2002-01-01

    X-ray magnetic diffraction experiment of ferromagnets that utilizes elliptically polarized synchrotron radiation is presented. First we have reviewed shortly historical backgrounds and theoretical aspects of the experiment. We have presented how the magnetic form factors are measured and are separated into the spin-moment component and the orbital-moment component in this experiment. Peculiar features of the polarization factor of this experiment have been explained. We have introduced two examples of the experiment. One is the measurement of the spin-magnetic form factor of SmAl sub 2 with white X-rays from a bending magnet at the Photon Factory. The other is the measurement of the orbital-magnetic form factor of Holmium Iron Garnets with monochromatic X-rays from an undulator at the SPring-8. Finally we summarize the article and show some future prospects of this experiment. (author)

  9. Single-pulse x-ray diffraction using polycapillary optics for in situ dynamic diffraction.

    Science.gov (United States)

    Maddox, B R; Akin, M C; Teruya, A; Hunt, D; Hahn, D; Cradick, J; Morgan, D V

    2016-08-01

    Diagnostic use of single-pulse x-ray diffraction (XRD) at pulsed power facilities can be challenging due to factors such as the high flux and brightness requirements for diffraction and the geometric constraints of experimental platforms. By necessity, the x-ray source is usually positioned very close, within a few inches of the sample. On dynamic compression platforms, this puts the x-ray source in the debris field. We coupled x-ray polycapillary optics to a single-shot needle-and-washer x-ray diode source using a laser-based alignment scheme to obtain high-quality x-ray diffraction using a single 16 ns x-ray pulse with the source >1 m from the sample. The system was tested on a Mo sample in reflection geometry using 17 keV x-rays from a Mo anode. We also identified an anode conditioning effect that increased the x-ray intensity by 180%. Quantitative measurements of the x-ray focal spot produced by the polycapillary yielded a total x-ray flux on the sample of 3.3 ± 0.5 × 10(7) molybdenum Kα photons.

  10. Wavefront aberrations of x-ray dynamical diffraction beams.

    Science.gov (United States)

    Liao, Keliang; Hong, Youli; Sheng, Weifan

    2014-10-01

    The effects of dynamical diffraction in x-ray diffractive optics with large numerical aperture render the wavefront aberrations difficult to describe using the aberration polynomials, yet knowledge of them plays an important role in a vast variety of scientific problems ranging from optical testing to adaptive optics. Although the diffraction theory of optical aberrations was established decades ago, its application in the area of x-ray dynamical diffraction theory (DDT) is still lacking. Here, we conduct a theoretical study on the aberration properties of x-ray dynamical diffraction beams. By treating the modulus of the complex envelope as the amplitude weight function in the orthogonalization procedure, we generalize the nonrecursive matrix method for the determination of orthonormal aberration polynomials, wherein Zernike DDT and Legendre DDT polynomials are proposed. As an example, we investigate the aberration evolution inside a tilted multilayer Laue lens. The corresponding Legendre DDT polynomials are obtained numerically, which represent balanced aberrations yielding minimum variance of the classical aberrations of an anamorphic optical system. The balancing of classical aberrations and their standard deviations are discussed. We also present the Strehl ratio of the primary and secondary balanced aberrations.

  11. Observation of sagittal X-ray diffraction by surface acoustic waves in Bragg geometry.

    Science.gov (United States)

    Vadilonga, Simone; Zizak, Ivo; Roshchupkin, Dmitry; Evgenii, Emelin; Petsiuk, Andrei; Leitenberger, Wolfram; Erko, Alexei

    2017-04-01

    X-ray Bragg diffraction in sagittal geometry on a Y-cut langasite crystal (La3Ga5SiO14) modulated by Λ = 3 µm Rayleigh surface acoustic waves was studied at the BESSY II synchrotron radiation facility. Owing to the crystal lattice modulation by the surface acoustic wave diffraction, satellites appear. Their intensity and angular separation depend on the amplitude and wavelength of the ultrasonic superlattice. Experimental results are compared with the corresponding theoretical model that exploits the kinematical diffraction theory. This experiment shows that the propagation of the surface acoustic waves creates a dynamical diffraction grating on the crystal surface, and this can be used for space-time modulation of an X-ray beam.

  12. Measuring the x-ray resolving power of bent potassium acid phthalate diffraction crystalsa)

    Science.gov (United States)

    Haugh, M. J.; Wu, M.; Jacoby, K. D.; Loisel, G. P.

    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 in Albuquerque, New Mexico. 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 double crystal diffractometer 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.

  13. 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.

  14. Radiation damage free two-color X-ray ghost diffraction with atomic resolution

    CERN Document Server

    Li, Zheng; Chapman, Henry; Shih, Yanhua

    2015-01-01

    The X-ray free electron lasers (XFEL) can enable diffractive structural determination of protein crystals or single molecules that are too small and radiation-sensitive for conventional X-ray analysis. However the electronic form factor could have been modified during the ultrashort X-ray pulse due to photoionization and electron cascade caused by the intense X-ray pulse. For general X-ray imaging techniques, to minimize radiation damage effect is of major concern to ensure faithful reconstruction of the structure. Here we show that a radiation damage free diffraction can be achieved with an atomic spatial resolution, by using X-ray parametric down-conversion (PDC), and two-color biphoton ghost imaging. We illustrate that formation of the diffractive patterns satisfies a condition analogous to the Bragg equation, with a resolution that could be as fine as the lattice length scale of several Angstrom. Because the samples are illuminated by the optical photons of low energy, they can be free of radiation damage...

  15. X-ray and Electron Diffraction Study of MgO

    NARCIS (Netherlands)

    Tsirelson, V.G.; Asilov, A.S.; Abramov, Yu. A.; Belokoneva, E.L.; Kitaneh, R.; Feil, D.

    1998-01-01

    Precise X-ray and high-energy transmission electron diffraction methods were used for the study of electron density and electrostatic potential in MgO crystals. The structure amplitudes were determined and their accuracy estimated using ab initio Hartree-Fock structure amplitudes as criteria. The el

  16. Electrostatic Molecular Interaction from X-ray Diffraction Data. II. Test on Theoretical Pyrazine Data

    NARCIS (Netherlands)

    Feil, Dirk; Moss, Grant

    1983-01-01

    In a previous paper [Moss & Feil (1981). Acta Cryst. A37, 414-421] a method was reported to calculate the electrostatic potential and the electrostatic interaction energy from single-crystal X-ray diffraction data. The method was applied to experimental pyrazine data; however, owing to the relativel

  17. An X-ray diffraction study of direct-bonded silicon interfaces

    DEFF Research Database (Denmark)

    Howes, P.B.; Benamara, M.; Grey, F.

    1998-01-01

    Semiconductor wafer bonding techniques have been used to create a giant twist grain boundary from two Si(001) wafers. We show, using X-ray diffraction measurements that after annealing the interface forms a highly ordered superstructure with relaxations extending to many layers into the crystals...

  18. 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.

  19. Spectrometer for Hard X-Ray Free Electron Laser Based on Diffraction Focusing

    CERN Document Server

    Kohn, V G; Vartanyants, I A

    2012-01-01

    X-ray free electron lasers (XFELs) generate sequences of ultra-short, spatially coherent pulses of x-ray radiation. We propose the diffraction focusing spectrometer (DFS), which is able to measure the whole energy spectrum of the radiation of a single XFEL pulse with an energy resolution of $\\Delta E/E\\approx 2\\times 10^{-6}$. This is much better than for most modern x-ray spectrometers. Such resolution allows one to resolve the fine spectral structure of the XFEL pulse. The effect of diffraction focusing occurs in a single crystal plate due to dynamical scattering, and is similar to focusing in a Pendry lens made from the metamaterial with a negative refraction index. Such a spectrometer is easier to operate than those based on bent crystals. We show that the DFS can be used in a wide energy range from 5 keV to 20 keV.

  20. New-corrected functions of X-ray powder diffraction

    Institute of Scientific and Technical Information of China (English)

    ZHANG QingLi; LIU WenPeng; DING LiHua; JIANG HaiHe; YIN ShaoTang

    2009-01-01

    X-ray powder diffraction is an indispensable technique to study material structure,phase transition and so on.It is necessary for high quality diffraction data to get high-precision diffraction angle.This work proposed four corrected functions of X-ray powder diffraction angle.Two methods,linearization method and modified Levenberg-Marquardt iteration method,are given to solve the function parameters,and the modified Levenberg-Marquardt method has fast convergent speed and stable solution.Two methods can give closed parameters,including those of Lu,Liu,and Chu functions and polynomial.New-corrected functions were used to fit the diffraction angle error of the tetragonal rutile polycrystalline TiO_2 mixed with Gd_(0.45)Y_(2.55)Sc_2Ga_3O_(12) as a standard sample,and the computation result indicates that these functions can characterize the diffraction error very well.In some cases,the new-corrected functions can describe the diffraction angle error better than the reported corrected functions.At the same time,the lattice parameter of Gd_(0.45)Y_(2.55)Sc_2Ga_3O_(12) was computed with two methods.When the corrected function parameters and lattice parameters were solved by the least square method,the interaction of the function parameters and lattice parameters would result in great error.However,when the X-ray diffraction angles were corrected by corrected functions using a standard sample,the authentic lattice parameters can be obtained by the least square fitting.

  1. Structural and magnetic properties of inverse opal photonic crystals studied by x-ray diffraction, scanning electron microscopy, and small-angle neutron scattering

    NARCIS (Netherlands)

    Grigoriev, S.V.; Napolskii, K.S.; Grigoryeva, N.A.; Vasilieva, A.V.; Mistonov, A.A.; Chernyshov, D.Y.; Petukhov, A.V.; Belov, D.V.; Eliseev, A.A.; Lukashin, A.V.; Tretyakov, Y.D.; Sinitskii, A.S.; Eckerlebe, H.

    2009-01-01

    The structural and magnetic properties of nickel inverse opal photonic crystal have been studied by complementary experimental techniques, including scanning electron microscopy, wide-angle and small-angle diffraction of synchrotron radiation, and polarized neutrons. The sample was fabricated by ele

  2. An analytical model for the determination of crystallite size and crystal lattice microstrain distributions in nanocrystalline materials from the variance of the X-ray diffraction peaks

    Energy Technology Data Exchange (ETDEWEB)

    Sanchez-Bajo, F. [Universidad de Extremadura, Departamento de Fisica Aplicada, Badajoz (Spain); Ortiz, A.L. [Universidad de Extremadura, Departamento de Ingenieria Mecanica, Energetica y de los Materiales, Badajoz (Spain); Cumbrera, F.L. [Universidad de Extremadura, Departamento de Fisica, Badajoz (Spain)

    2009-01-15

    An analytical model for the determination of crystallite size and crystal lattice microstrain distributions in nanocrystalline (nc) materials by X-ray diffractometry (XRD) is presented. It entails generalizing the variance method to establish analytically the connection between the variance coefficients of the physically broadened XRD peaks and the characteristic parameters of explicit distributions of crystallite sizes and crystal lattice microstrains, which results in a more detailed characterization of the nc-materials. The proposed model is generic in nature and has the potential to be used under the assumption of different mathematical functions for the two distributions, which suggests that it may have an important role to play in the characterization of nc-materials. Nevertheless, the specialization to the case of nc-materials with log-normal crystallite size distribution and three typical types of lattice microstrains is used as an illustration and to formulate explicit analytical expressions of interest. Finally, the usefulness of the proposed model is demonstrated on standard XRD profiles. (orig.)

  3. Focal construct geometry for high intensity energy dispersive x-ray diffraction based on x-ray capillary optics.

    Science.gov (United States)

    Li, Fangzuo; Liu, Zhiguo; Sun, Tianxi; Jiang, Bowen; Zhu, Yu

    2016-03-14

    We presented a focal construct geometry (FCG) method for high intensity energy dispersive X-ray diffraction by utilizing a home-made ellipsoidal single-bounce capillary (ESBC) and a polycapillary parallel X-ray lens (PPXRL). The ESBC was employed to focus the X-rays from a conventional laboratory source into a small focal spot and to produce an annular X-ray beam in the far-field. Additionally, diffracted polychromatic X-rays were confocally collected by the PPXRL attached to a stationary energy-resolved detector. Our FCG method based on ESBC and PPXRL had achieved relatively high intensity diffraction peaks and effectively narrowed the diffraction peak width which was helpful in improving the potential d-spacing resolution for material phase analysis.

  4. X-ray diffraction study of directionally grown perylene crystallites

    DEFF Research Database (Denmark)

    Breiby, Dag W.; Lemke, H. T.; Hammershøj, P.

    2008-01-01

    Using grazing incidence X-ray diffraction, perylene crystallites grown on thin highly oriented poly(tetrafluoroethylene) (PTFE) films on silicon substrates have been investigated. All the perylene crystallites are found to orient with the ab plane of the monoclinic unit cell parallel to the subst......Using grazing incidence X-ray diffraction, perylene crystallites grown on thin highly oriented poly(tetrafluoroethylene) (PTFE) films on silicon substrates have been investigated. All the perylene crystallites are found to orient with the ab plane of the monoclinic unit cell parallel...... to the substrate. The scattering data is interpreted as a trimodal texture of oriented perylene crystallites, induced by interactions between the perylene molecules and the oriented PTFE substrate. Three families of biaxial orientations are seen, with the axes (h = 1, 2, or 3) parallel to the PTFE alignment......, all having the ab-plane parallel to the substrate. About 92% of the scattered intensity corresponds to a population with highly parallel to (PTFE)....

  5. Structured illumination for tomographic X-ray diffraction imaging.

    Science.gov (United States)

    Greenberg, Joel A; Hassan, Mehadi; Krishnamurthy, Kalyani; Brady, David

    2014-02-21

    Tomographic imaging of the molecular structure of an object is important for a variety of applications, ranging from medical and industrial radiography to security screening. X-ray diffraction imaging is the preeminent technique for performing molecular analysis of large volumes. Here we propose and demonstrate a new measurement architecture to improve the source and detector efficiency for diffraction imaging. In comparison with previous techniques, our approach reduces the required overall scan time by 1-2 orders of magnitude, which makes possible real-time scanning of a broad range of materials over a large volume using a table-top setup. This method, which relies on structuring spatially the illumination incident on an object moving relative to the X-ray source, is compatible with existing systems and has the potential to significantly enhance performance in an array of areas, such as medical diagnostic imaging and explosives detection.

  6. Crystallization and preliminary X-ray diffraction studies of the complete modular endolysin from Cp-1, a phage infecting Streptococcus pneumoniae.

    Science.gov (United States)

    Monterroso, Begoña; Albert, Armando; Martínez-Ripoll, Martín; García, Pedro; García, José Luis; Menéndez, Margarita; Hermoso, Juan A

    2002-09-01

    Endolysin from the phage Cp-1 (Cpl-1) cleaves the glycosidic beta1,4-bonds between the N-acetylmuramic acid and the N-acetylglucosamine of the pneumococcal cell wall. Cpl-1 has been crystallized using the hanging-drop vapour-diffusion method at 291 K. Diffraction-quality orthorhombic crystals of the native protein were obtained only after addition of the detergent n-decyl-beta-D-maltoside. Crystals belong to space group C222(1), with unit-cell parameters a = 77.949, b = 95.782, c = 129.282 A. Diffraction data to a resolution of 2.1 A were collected at a synchrotron facility.

  7. 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.

  8. DIFFRACTION FROM MODEL CRYSTALS

    Science.gov (United States)

    Although calculating X-ray diffraction patterns from atomic coordinates of a crystal structure is a widely available capability, calculation from non-periodic arrays of atoms has not been widely applied to cellulose. Non-periodic arrays result from modeling studies that, even though started with at...

  9. X-ray diffraction from single GaAs nanowires

    Energy Technology Data Exchange (ETDEWEB)

    Biermanns, Andreas

    2012-11-12

    In recent years, developments in X-ray focussing optics have allowed to produce highly intense, coherent X-ray beams with spot sizes in the range of 100 nm and below. Together with the development of new experimental stations, X-ray diffraction techniques can now be applied to study single nanometer-sized objects. In the present work, X-ray diffraction is applied to study different aspects of the epitaxial growth of GaAs nanowires. Besides conventional diffraction methods, which employ X-ray beams with dimensions of several tens of {mu}m, special emphasis lies on the use of nanodiffraction methods which allow to study single nanowires in their as-grown state without further preparation. In particular, coherent X-ray diffraction is applied to measure simultaneously the 3-dimensional shape and lattice parameters of GaAs nanowires grown by metal-organic vapor phase epitaxy. It is observed that due to a high density of zinc-blende rotational twins within the nanowires, their lattice parameter deviates systematically from the bulk zinc-blende phase. In a second step, the initial stage in the growth of GaAs nanowires on Si (1 1 1) surfaces is studied. This nanowires, obtained by Ga-assisted growth in molecular beam epitaxy, grow predominantly in the cubic zinc-blende structure, but contain inclusions of the hexagonal wurtzite phase close to their bottom interface. Using nanodiffraction methods, the position of the different structural units along the growth axis is determined. Because the GaAs lattice is 4% larger than silicon, these nanowires release their lattice mismatch by the inclusion of dislocations at the interface. Whereas NWs with diameters below 50 nm are free of strain, a rough interface structure in nanowires with diameters above 100 nm prevents a complete plastic relaxation, leading to a residual strain at the interface that decays elastically along the growth direction. Finally, measurements on GaAs-core/InAs-shell nanowire heterostructures are presented

  10. 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.

  11. X-ray diffraction in temporally and spatially resolved biomolecular science.

    Science.gov (United States)

    Helliwell, John R; Brink, Alice; Kaenket, Surasak; Starkey, Victoria Laurina; Tanley, Simon W M

    2015-01-01

    Time-resolved Laue protein crystallography at the European Synchrotron Radiation Facility (ESRF) opened up the field of sub-nanosecond protein crystal structure analyses. There are a limited number of such time-resolved studies in the literature. Why is this? The X-ray laser now gives us femtosecond (fs) duration pulses, typically 10 fs up to ∼50 fs. Their use is attractive for the fastest time-resolved protein crystallography studies. It has been proposed that single molecules could even be studied with the advantage of being able to measure X-ray diffraction from a 'crystal lattice free' single molecule, with or without temporal resolved structural changes. This is altogether very challenging R&D. So as to assist this effort we have undertaken studies of metal clusters that bind to proteins, both 'fresh' and after repeated X-ray irradiation to assess their X-ray-photo-dynamics, namely Ta6Br12, K2PtI6 and K2PtBr6 bound to a test protein, hen egg white lysozyme. These metal complexes have the major advantage of being very recognisable shapes (pseudo spherical or octahedral) and thereby offer a start to (probably very difficult) single molecule electron density map interpretations, both static and dynamic. A further approach is to investigate the X-ray laser beam diffraction strength of a well scattering nano-cluster; an example from nature being the iron containing ferritin. Electron crystallography and single particle electron microscopy imaging offers alternatives to X-ray structural studies; our structural studies of crustacyanin, a 320 kDa protein carotenoid complex, can be extended either by electron based techniques or with the X-ray laser representing a fascinating range of options. General outlook remarks concerning X-ray, electron and neutron macromolecular crystallography as well as 'NMR crystallography' conclude the article.

  12. Portable energy dispersive X-ray fluorescence and X-ray diffraction and radiography system for archaeometry

    Energy Technology Data Exchange (ETDEWEB)

    Mendoza Cuevas, Ariadna, E-mail: ariadna@mail.or [Archaeometry Laboratory, Colegio Universitario San Geronimo de La Habana, Obispo, entre San Ignacio y Mercaderes, Habana Vieja, cp 10 100, Havana (Cuba); Perez Gravie, Homero, E-mail: homero.perezgravie@mail.co [Archaeometry Laboratory, Colegio Universitario San Geronimo de La Habana, Obispo, entre San Ignacio y Mercaderes, Habana Vieja, cp 10 100, Havana (Cuba)

    2011-03-21

    Starting on a laboratory developed portable X-ray fluorescence (PXRF) spectrometer; three different analytical results can be performed: analysis of chemical elements, analysis of major chemical crystalline phase and structural analysis, which represents a contribution to a new, low cost development of portable X-ray analyzer; since these results are respectively obtained with independent equipments for X-ray fluorescence, X-ray diffraction and radiography. Detection limits of PXRF were characterized using standard reference materials for ceramics, glass, bronze and bones, which are the main materials requiring quantitative analysis in art and archeological objects. A setup for simultaneous energy dispersive X-ray fluorescence and diffraction (ED (XRF-XRD)) in the reflection mode has been tested for in situ and non-destructive analysis according to the requirements of art objects inspection. The system uses a single low power X-ray tube and an X-ray energy dispersive detector to measure X-ray diffraction spectrum at a fixed angle. Application to the identification of jadeite-jade mineral in archeological objects by XRD is presented. A local high resolution radiography image obtained with the same low power X-ray tube allows for studies in painting and archeological bones.

  13. Observation of parametric X-ray radiation in an anomalous diffraction region

    Energy Technology Data Exchange (ETDEWEB)

    Alexeyev, V.I., E-mail: vial@x4u.lebedev.ru [P.N. Lebedev Physical Institute RAS, 53 Leninskiy prospect, Moscow (Russian Federation); Belgorod National Research University, 85 Pobedy st., Belgorod (Russian Federation); Eliseyev, A.N., E-mail: elisseev@pluton.lpi.troitsk.ru [P.N. Lebedev Physical Institute RAS, 53 Leninskiy prospect, Moscow (Russian Federation); Belgorod National Research University, 85 Pobedy st., Belgorod (Russian Federation); Irribarra, E., E-mail: esteban.irribarra@epn.edu.ec [Escuela Politécnica Nacional, Ladrón de Guevara E11-253, Quito (Ecuador); Kishin, I.A., E-mail: ivan.kishin@mail.ru [P.N. Lebedev Physical Institute RAS, 53 Leninskiy prospect, Moscow (Russian Federation); Belgorod National Research University, 85 Pobedy st., Belgorod (Russian Federation); Kubankin, A.S., E-mail: kubankin@bsu.edu.ru [P.N. Lebedev Physical Institute RAS, 53 Leninskiy prospect, Moscow (Russian Federation); Belgorod National Research University, 85 Pobedy st., Belgorod (Russian Federation); Nazhmudinov, R.M., E-mail: fizeg@bk.ru [P.N. Lebedev Physical Institute RAS, 53 Leninskiy prospect, Moscow (Russian Federation); Belgorod National Research University, 85 Pobedy st., Belgorod (Russian Federation)

    2016-08-19

    A new possibility to expand the energy region of diffraction processes based on the interaction of relativistic charged particles with crystalline structures is presented. Diffracted photons related to parametric X-ray radiation produced by relativistic electrons are detected below the low energy threshold for the X-ray diffraction mechanism in crystalline structures for the first time. The measurements were performed during the interaction of 7 MeV electrons with a textured polycrystalline tungsten foil and a highly oriented pyrolytic graphite crystal. The experiment results are in good agreement with a developed model based on the PXR kinematical theory. The developed experimental approach can be applied to separate the contributions of real and virtual photons to the total diffracted radiation generated during the interaction of relativistic charged particles with crystalline targets. - Highlights: • Parametric X-ray radiation below the low energy threshold for diffraction of free X-rays. • Experimental separation of the contributions from different radiation mechanisms. • PXR from relativistic electrons in mosaic crystals and textured polycrystlas.

  14. Syntheses, Vibrational Spectroscopy, and Crystal Structure Determination from X-Ray Powder Diffraction Data of Alkaline Earth Dicyanamides M[N(CN)

    Energy Technology Data Exchange (ETDEWEB)

    Juergens, Barbara; Irran, Elisabeth; Schnick, Wolfgang

    2001-03-01

    The alkaline earth dicyanamides Mg[N(CN){sub 2}]{sub 2}, Ca[N(CN){sub 2}]{sub 2}, Sr[N(CN){sub 2}]{sub 2}, and Ba[N(CN){sub 2}]{sub 2} were synthesized by ion exchange using Na[N(CN){sub 2}] and the respective nitrates or bromides as starting materials. The crystal structures were determined from X-ray powder diffractometry: Mg[N(CN){sub 2}]{sub 2}, Pnnm, Z=2, a=617.14(3), b=716.97(3), and c=740.35(5) pm; Ca[N(CN){sub 2}]{sub 2} and Sr[N(CN){sub 2}]{sub 2}, C2/c, Z=4; Ca[N(CN){sub 2}]{sub 2}, a=1244.55(3), b=607.97(1), and c=789.81(1) pm, {beta}=98.864(2){degree}; Sr[N(CN){sub 2}]{sub 2}, a=1279.63(2), b=624.756(8), and c=817.56(1) pm, {beta}=99.787(1){degree}; Ba[N(CN){sub 2}]{sub 2}, Pnma, Z=4, a=1368.68(7), b=429.07(7), and c=1226.26(2) pm. The dicyanamides consist of the respective alkaline earth cations and bent planar [N(CN){sub 2}]{sup -} ions. The structural features were correlated with vibrational spectroscopic data. The thermal behavior was studied by thermoanalytical experiments.

  15. Design and performance of an imaging plate system for X-ray diffraction study

    Science.gov (United States)

    Amemiya, Yoshiyuki; Matsushita, Tadashi; Nakagawa, Atsushi; Satow, Yoshinori; Miyahara, Junji; Chikawa, Jun-ichi

    1988-04-01

    A new readout system for a BaFBr: Eu 2+ photostimulable phosphor screen (imaging plate) was constructed by modifying a drum scanner, with a design optimized for X-ray diffraction and scattering applications. An effort was made to achieve a high detective quantum efficiency below 20 keV, a small pixel size (25 μm × 25 μm), a low quantization noise (0.22%) using 12-bit A/D converters, and the capability to cover an inherent dynamic range (1:10 5) of the photostimulated luminescence by using two photomultiplier tubes. This system is being used in several synchrotron radiation experiments: Laue diffraction of protein crystals, small angle diffraction from a single muscle fiber, powder diffraction from crystals in a diamond anvil cell, and time-resolved small-angle X-ray scattering from a synthetic polymer during stretching.

  16. 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.

  17. Simulating X-ray diffraction of textured films

    DEFF Research Database (Denmark)

    Breiby, Dag W.; Bunk, Oliver; Andreasen, Jens Wenzel

    2008-01-01

    Computationally efficient simulations of grazing-incidence X-ray diffraction (GIXD) are discussed, with particular attention given to textured thin polycrystalline films on supporting substrates. A computer program has been developed for simulating scattering from thin films exhibiting varying...... from the totally substrate-reflected beam ( two-beam approximation) and refraction effects are also included in the program, together with the geometrical intensity corrections associated with GIXD measurements. To achieve 'user friendliness' for scientists less familiar with diffraction......, the mathematically simplest possible descriptions are sought whenever feasible. The practical use of the program is demonstrated for a selected thin-film example, perylene, which is of relevance for organic electronics....

  18. 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}.

  19. Crystallization and preliminary X-ray diffraction studies of a toxic phospholipase A2 from the venom of Vipera ammodytes meridionalis complexed to a synthetic inhibitor.

    Science.gov (United States)

    Georgieva, Dessislava Nikolova; Rypniewski, Wojciech; Perbandt, Markus; Jain, Mahendra; Genov, Nicolay; Betzel, Christian

    2003-08-21

    A toxic phospholipase A(2) (PLA(2)) is isolated from the neurotoxic complex Vipoxin, the major lethal component of the venom of Vipera ammodytes meridionalis. The enzyme is complexed to the synthetic inhibitor elaidoylamide and crystallized. The crystals belong to the space group P2(1)2(1)2(1), with unit cell dimensions a=46.57 A, b=82.68 A, c=119.47 A and beta=90 degrees. Initial diffraction data to 3.3 A resolution are collected.

  20. Crystal chemistry of nephelines from ijolites and nepheline-rich pegmatites: influence of composition and genesis on the crystal structure investigated by X-ray diffraction

    DEFF Research Database (Denmark)

    Vulić, Predrag; Balić-Žunić, Tonči; Belmonte, Louise Josefine;

    2011-01-01

    some degree of disorder in the Si/Al distribution. Most of the samples revealed a practically full Si-Al-ordering, but the crystals from one of the nepheline-syenite pegmatites in Langesundsfjord, Norway and from the type locality of ijolite, Iivaara, Finland, showed a disorder of 10–20% suggesting...

  1. Crystal chemistry of nephelines from ijolites and nepheline-rich pegmatites: influence of composition and genesis on the crystal structure investigated by X-ray diffraction

    DEFF Research Database (Denmark)

    Vulic, Predrag; Balic Zunic, Tonci; Belmonte, Louise Josefine;

    2011-01-01

    some degree of disorder in the Si/Al distribution. Most of the samples revealed a practically full Si-Alordering, but the crystals from one of the nepheline-syenite pegmatites in Langesundsfjord, Norway and from the type locality of ijolite, Iivaara, Finland, showed a disorder of 10–20% suggesting...

  2. 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.

  3. An ultrahigh-vacuum chamber for surface X-ray diffraction combined with MBE

    Science.gov (United States)

    Vlieg, E.; Van't Ent, A.; De Jongh, A. P.; Neerings, H.; Van Der Veen, J. F.

    1987-12-01

    An ultrahigh-vacuum chamber has been built which can be coupled to a diffractometer via a rotary feedthrough. X-rays enter and leave the chamber through a large beryllium window. In addition to standard equipment for surface preparation and reflection high-energy electron diffraction, the chamber contains Knudsen evaporation cells for MBE crystal growth. This arrangement allows in situ diffraction experiments to be performed on growing surfaces and thin films.

  4. Pressure-induced phase transitions in organic molecular crystals: a combination of x-ray single-crystal and powder diffraction, raman and IR-spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Boldyreva, E V; Goryainov, S V; Seryotkin, Y V; Kolesnik, E N; Shakhtshneider, T P; Ivashevskaya, S N; Drebushchak, T N [Research and Education Center ' Molecular Design and Ecologically Safe Technologies' , REC-008, Novosibirsk State University (Russian Federation); Sowa, H [Goettingen University (Germany); Ahsbahs, H; Chernyshev, V V [Marburg University (Germany); Dmitriev, V P [Swiss-Norwegian Beamline ESRF, Grenoble (France)], E-mail: boldyrev@nsu.ru

    2008-07-15

    The contribution summarizes the results of recent studies of phase transitions induced by high pressure in a number of molecular organic crystals, such as polymorphs of paracetamol, chlorpropamide, polymorphs of glycine, L- and DL-serine, {beta}-alanine. The main attention is paid to the following topics: (1) Reversible / irreversible transformations; (2) Different behavior of single crystals / powders; (3) The role of pressure-transmitting liquid; (4) The role of the kinetic factors: phase transitions on decompression, or after a long storage at a selected pressure; (5) Isosymmetric phase transitions; (6) The role of the changes in the hydrogen bond networks / intramolecular conformational changes in the phase transitions; (7) Superstructures / nanostructures formed as a result of pressure-induced phase transitions.

  5. Complementing high-throughput X-ray powder diffraction data with quantum-chemical calculations

    DEFF Research Database (Denmark)

    Naelapaa, Kaisa; van de Streek, Jacco; Rantanen, Jukka

    2012-01-01

    High-throughput crystallisation and characterisation platforms provide an efficient means to carry out solid-form screening during the pre-formulation phase. To determine the crystal structures of identified new solid phases, however, usually requires independent crystallisation trials to produce...... single crystals or bulk samples of sufficient quantity to carry out high-quality X-ray diffraction measurements. This process could be made more efficient by a robust procedure for crystal structure determination directly from high-throughput X-ray powder diffraction (XRPD) data. Quantum......-chemical calculations based on dispersion-corrected density functional theory (DFT-D) have now become feasible for typical small organic molecules used as active pharmaceutical ingredients. We demonstrate how these calculations can be applied to complement high-throughput XRPD data by determining the crystal structure...

  6. Serial femtosecond X-ray diffraction of enveloped virus microcrystals

    Directory of Open Access Journals (Sweden)

    Robert M. Lawrence

    2015-07-01

    Full Text Available Serial femtosecond crystallography (SFX using X-ray free-electron lasers has produced high-resolution, room temperature, time-resolved protein structures. We report preliminary SFX of Sindbis virus, an enveloped icosahedral RNA virus with ∼700 Å diameter. Microcrystals delivered in viscous agarose medium diffracted to ∼40 Å resolution. Small-angle diffuse X-ray scattering overlaid Bragg peaks and analysis suggests this results from molecular transforms of individual particles. Viral proteins undergo structural changes during entry and infection, which could, in principle, be studied with SFX. This is an important step toward determining room temperature structures from virus microcrystals that may enable time-resolved studies of enveloped viruses.

  7. 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%.

  8. 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.

  9. Controlled molecules for X-ray diffraction experiments at free-electron lasers

    Energy Technology Data Exchange (ETDEWEB)

    Stern, Stephan

    2013-12-15

    X-ray diffractive imaging is at the very heart of materials science and has been utilized for decades to solve unknown molecular structures. Nowadays, it serves as the key method of structural biology to solve molecular structures of large biological molecules comprising several thousand or even millions of atoms. However, X-ray diffraction from isolated molecules is very weak. Therefore, the regular and periodic arrangement of a huge number of identical copies of a certain molecule of interest within a crystal lattice has been a necessary condition in order to exploit Bragg diffraction of X-rays. This results in a huge increase in scattered signal and a strongly improved signal-to-noise ratio compared to diffraction from non-crystalline samples. The major bottleneck of structural biology is that many of biologically interesting molecules refuse to form crystals of sufficient size to be used at synchrotron X-ray lightsources. However, novel X-ray free-electron lasers (XFELs), which became operational very recently, promise to address this issue. X-ray pulses provided by XFELs are many orders of magnitude more intense than X-ray pulses from a synchrotron source and at the same time as short as only several tens of femtoseconds. Combined with wavelengths in the nm-pm range, XFELs are well-suited to study ultrafast atomic and molecular dynamics. Additionally, the ultrashort pulses can be utilized to circumvent the damage threshold which set a limit to the incident intensity in X-ray diffraction experiments before. At XFELs, though eventually destroying the investigated sample, no significant sample deterioration happens on the ultrashort timescale of the XFEL pulse and the measured diffraction pattern is due to an (almost) unharmed sample. In the framework of this thesis, the approach of utilizing the highly intense XFEL pulses for X-ray diffraction of weakly-scattering non-crystalline samples was taken to the limit of small isolated molecules. X-ray diffraction was

  10. Nano-structured titanium and aluminium nitride coatings: Study by grazing incidence X-ray diffraction and X-ray absorption and anomalous diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Tuilier, M.-H., E-mail: marie-helene.tuilier@uha.fr [Universite de Haute Alsace (UHA), Laboratoire Physique et Mecanique Textile (LPMT), EA 4365 -conventionnee au CNRS, Equipe PPMR, F-68093 Mulhouse (France); Pac, M.-J. [Universite de Haute Alsace (UHA), Laboratoire Physique et Mecanique Textile (LPMT), EA 4365 - conventionnee au CNRS, Equipe PPMR, F-68093 Mulhouse (France); Anokhin, D.V. [Universite de Haute Alsace (UHA), CNRS, Institut de Science des Materiaux de Mulhouse (IS2M), LRC 7228, F-68093 Mulhouse (France); Moscow State University, Faculty of Fundamental Physical and Chemical Engineering, 119991, Moscow, GSP-1, 1-51 Leninskie Gory (Russian Federation); Ivanov, D.A. [Universite de Haute Alsace (UHA), CNRS, Institut de Science des Materiaux de Mulhouse (IS2M), LRC 7228, F-68093 Mulhouse (France); Rousselot, C. [Universite de Franche-Comte, FEMTO-ST (UMR CNRS 6174), F-25211 Montbeliard (France); Thiaudiere, D. [Synchrotron Soleil, Saint Aubin, F-91192 Gif sur Yvette (France)

    2012-12-30

    Titanium and aluminium nitride thin films, Ti{sub 1-x}Al{sub x}N (x = 0, x = 0.5, x = 0.68), deposited by reactive magnetron sputtering on silicon substrates are investigated by combining two different X-ray diffraction experiments carried out using synchrotron radiation. Grazing-incidence X-ray diffraction and Ti K-edge diffraction anomalous near edge structure spectroscopy provide information on the micro- and nano-structure of the films respectively, which play a crucial role in the functionality of coatings. The spectroscopic data of Ti{sub 0.50}Al{sub 0.50}N film show that Ti atoms in crystallized domains and grain boundaries are all in octahedral cubic local order, but their growth mode is quite different. It is found that the crystallized part of the Ti{sub 0.50}Al{sub 0.50}N film has a single-crystalline nature, whereas the TiN one presents a fibrillar microstructure. For Ti{sub 0.32}Al{sub 0.68}N film, grazing-incidence X-ray diffraction provides information on the uniaxial texture along the [001] direction of the hexagonal lattice. A sharp Ti K pre-edge peak is observed in diffraction anomalous near edge spectrum that definitely shows that Ti atoms are incorporated in the hexagonal lattice of those fibrillar domains. Moreover, the difference observed between Ti K-edge diffraction anomalous and X-ray absorption pre-edge regions proves that a significant part of Ti atoms is located in nanocrystallites with cubic symmetry outside of the crystallized domains. - Highlights: Black-Right-Pointing-Pointer We study nano and micro-structures of TiN, Ti{sub 0.50}Al{sub 0.50}N and Ti{sub 0.32}Al{sub 0.68}N films. Black-Right-Pointing-Pointer Anomalous diffraction solves the crystallized part regardless of grain boundaries. Black-Right-Pointing-Pointer TiN microstructure is fibrillar, Ti{sub 0.5}Al{sub 0.5}N presents single crystalline domains. Black-Right-Pointing-Pointer For Ti{sub 0.32}Al{sub 0.68}N, Ti atoms are located in nanocrystallites with cubic symmetry

  11. Identifications studies of Lauha Bhasma by X-ray diffraction and X-ray fluorescence

    Science.gov (United States)

    Bhargava, S. C.; Reddy, K. R. C; Sastry, G. V. S

    2012-01-01

    Procedures for preparation of Lauha Bhasma are described in ancient texts of Ayurveda. These procedures also begin with different source material for iron such as Teekshna Lauha and Kanta Lauha etc. In the present study, we have selected different source materials viz. magnetite iron ore for Kanta Lauha and pure (Armco grade) iron turnings for Teekshna Lauha. The standard procedures of preparation of Lauha Bhasma are carried out in identical conditions for these two raw materials. The final product from the Puta are characterized by using X-ray diffraction and X-ray fluorescence spectroscopy to understanding the crystallographic form or forms of iron oxides and their composition at the end of each Puta. The iron content at the end of repeated Putas (18 for Kanta Lauha and 20 for Teekshna Lauha) have shown a decrease in case of Teekshna Lauha since the starting material is pure iron while it showed only marginal decreases in the case of Kanta Lauha because the Fe3O4 of magnetite is undergoing oxidation to Fe2O3. The trace elements remain within the Bhasma in the form of various oxides of Si, Al, Ca, etc. PMID:23049200

  12. Identifications studies of Lauha Bhasma by X-ray diffraction and X-ray fluorescence.

    Science.gov (United States)

    Bhargava, S C; Reddy, K R C; Sastry, G V S

    2012-01-01

    Procedures for preparation of Lauha Bhasma are described in ancient texts of Ayurveda. These procedures also begin with different source material for iron such as Teekshna Lauha and Kanta Lauha etc. In the present study, we have selected different source materials viz. magnetite iron ore for Kanta Lauha and pure (Armco grade) iron turnings for Teekshna Lauha. The standard procedures of preparation of Lauha Bhasma are carried out in identical conditions for these two raw materials. The final product from the Puta are characterized by using X-ray diffraction and X-ray fluorescence spectroscopy to understanding the crystallographic form or forms of iron oxides and their composition at the end of each Puta. The iron content at the end of repeated Putas (18 for Kanta Lauha and 20 for Teekshna Lauha) have shown a decrease in case of Teekshna Lauha since the starting material is pure iron while it showed only marginal decreases in the case of Kanta Lauha because the Fe(3)O(4) of magnetite is undergoing oxidation to Fe(2)O(3). The trace elements remain within the Bhasma in the form of various oxides of Si, Al, Ca, etc.

  13. An Inquiry Based Exercise Using X-ray Diffraction Data to Incite Student Learning

    Science.gov (United States)

    Rogow, D. L.; McDonald, W.; Bresler, M. R.

    2010-12-01

    An inquiry based learning exercise was designed for an upper division advanced inorganic laboratory course that meets one of the requirements for the Bachelor of Science degree in Chemistry and Biochemistry at the University of California, Santa Cruz. The content goals of this exercise were evaluation of whether a given solid state structure was previously known by using powder X-ray diffraction data, and understanding how the diffraction pattern relates to the crystal structure of the compound in question. The scientific process goals included searching a database to match the patterns and preparing data for oral presentations. The goals of the exercise were addressed via an activity allowing students to utilize real X-ray powder diffraction data to search and match with known structures in a database (International Crystal Structure Database) and to give an oral presentation. After students found their structures in the database, they prepared oral presentations justifying their choice for the match and their reasoning through structural analysis of the X-ray data. Students learned about X-ray diffraction theory in an inquiry type environment and gained valuable experience and confidence in presenting their findings using strong reasoning and communication skills. Assessment was implemented during active facilitation throughout the activity and during the final oral presentations.

  14. Advances in thin film diffraction instrumentation by X-ray optics

    Energy Technology Data Exchange (ETDEWEB)

    Haase, A. [Rich. Seifert and Co., Analytical X-ray Systems, Ahrensburg (Germany)

    1996-09-01

    The structural characterisation of thin films requires a parallel X-ray beam of high intensity. Parallel beam geometry is commonly used in high resolution and single crystal experiments, but also in the field of X-ray diffraction for polycrystalline material (e.g. in phase, texture and stress analysis). For grazing incidence diffraction (GID), the use of small slits on the primary side and of long soller slits with a flat monochromator on the secondary side is standard. New optical elements have been introduced with polychromatic or monochromatic radiation. By means of different applications the results are compared with those of classical beam optics. X-ray fiber optics utilize total external reflection of X-rays on smooth surfaces. Effects of monochromatization are presented. In many fields of application, fiber optics may replace conventional collimators. The use of primary and secondary channel cut crystals can also produce a high parallel monochromatic X-ray beam. A parabolically bent graded multilayer produces a monochromatic parallel beam of high intensity. Compared with classical Bragg-Brentano (focussing) geometry, excellent results have been obtained, especially for samples with an irregular shape. In combination with a channel cut monochromator there is a substantial gain in intensity leading to an increase of the dynamic intensity range of rocking curves.

  15. X-ray topography using the forward transmitted beam under multiple-beam diffraction conditions.

    Science.gov (United States)

    Tsusaka, Y; Takeda, S; Takano, H; Yokoyama, K; Kagoshima, Y; Matsui, J

    2016-02-01

    X-ray topographs are taken for a sapphire wafer with the [0001] surface normal, as an example, by forward transmitted synchrotron x-ray beams combined with two-dimensional electronic arrays in the x-ray detector having a spatial resolution of 1 μm. They exhibit no shape deformation and no position shift of the dislocation lines on the topographs. Since the topography is performed under multiple-beam diffraction conditions, the topographic images of a single diffraction (two-wave approximation condition) or plural diffractions (six-wave approximation condition) can be recorded without large specimen position changes. As usual Lang topographs, it is possible to determine the Burgers vector of each dislocation line. Because of high parallelism of the incoming x-rays and linear sensitivity of the electronic arrays to the incident x-rays, the present technique can be used to visualize individual dislocations in single crystals of the dislocation density as high as 1 × 10(5) cm(-2).

  16. 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.

  17. 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.

  18. 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...

  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. Combining operando synchrotron X-ray tomographic microscopy and scanning X-ray diffraction to study lithium ion batteries

    Science.gov (United States)

    Pietsch, Patrick; Hess, Michael; Ludwig, Wolfgang; Eller, Jens; Wood, Vanessa

    2016-01-01

    We present an operando study of a lithium ion battery combining scanning X-ray diffraction (SXRD) and synchrotron radiation X-ray tomographic microscopy (SRXTM) simultaneously for the first time. This combination of techniques facilitates the investigation of dynamic processes in lithium ion batteries containing amorphous and/or weakly attenuating active materials. While amorphous materials pose a challenge for diffraction techniques, weakly attenuating material systems pose a challenge for attenuation-contrast tomography. Furthermore, combining SXRD and SRXTM can be used to correlate processes occurring at the atomic level in the crystal lattices of the active materials with those at the scale of electrode microstructure. To demonstrate the benefits of this approach, we investigate a silicon powder electrode in lithium metal half-cell configuration. Combining SXRD and SRXTM, we are able to (i) quantify the dissolution of the metallic lithium electrode and the expansion of the silicon electrode, (ii) better understand the formation of the Li15Si4 phase, and (iii) non-invasively probe kinetic limitations within the silicon electrode. A simple model based on the 1D diffusion equation allows us to qualitatively understand the observed kinetics and demonstrates why high-capacity electrodes are more prone to inhomogeneous lithiation reactions. PMID:27324109

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Crystal structure of the quaternary compounds CuFe2AlSe4 and CuFe2GaSe4 from X-ray powder diffraction

    Indian Academy of Sciences (India)

    G E Delgado; A J Mora; P Grima-Gallardo; M Muñoz; S Durán; M Quintero; J M Briceño

    2015-08-01

    The crystal structure of the quaternary compounds CuFe2AlSe4 and CuFe2GaSe4, belonging to the system I–II2–III–VI4, were characterized using X-ray powder diffraction data. Both compounds crystallize in the tetragonal space group I42m (No. 121), = 2, with unit cell parameters = 5.609(1) Å, = 10.963(2) Å for CuFe2AlSe4 and = 5.6165(3) Å, = 11.075(1) Å for CuFe2GaSe4. These compounds are isostructural with CuFe2InSe4, and have a normal adamantane stannite structure.

  6. 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.

  7. 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.

  8. Fusion bonding of Si wafers investigated by x ray diffraction

    DEFF Research Database (Denmark)

    Weichel, Steen; Grey, Francois; Rasmussen, Kurt

    2000-01-01

    The interface structure of bonded Si(001) wafers with twist angle 6.5 degrees is studied as a function of annealing temperature. An ordered structure is observed in x-ray diffraction by monitoring a satellite reflection due to the periodic modulation near the interface, which results from...... the formation of a regular array of screw dislocations. This satellite reflection first appears at an annealing temperature of 800 degrees C, and increases abruptly up to temperatures of 1000 degrees C. We propose that this transition occurs when there is sufficient mobility for the reorganization of atomic...

  9. Observation of parametric X-ray radiation in an anomalous diffraction region

    Science.gov (United States)

    Alexeyev, V. I.; Eliseyev, A. N.; Irribarra, E.; Kishin, I. A.; Kubankin, A. S.; Nazhmudinov, R. M.

    2016-08-01

    A new possibility to expand the energy region of diffraction processes based on the interaction of relativistic charged particles with crystalline structures is presented. Diffracted photons related to parametric X-ray radiation produced by relativistic electrons are detected below the low energy threshold for the X-ray diffraction mechanism in crystalline structures for the first time. The measurements were performed during the interaction of 7 MeV electrons with a textured polycrystalline tungsten foil and a highly oriented pyrolytic graphite crystal. The experiment results are in good agreement with a developed model based on the PXR kinematical theory. The developed experimental approach can be applied to separate the contributions of real and virtual photons to the total diffracted radiation generated during the interaction of relativistic charged particles with crystalline targets.

  10. Twisted X-rays: incoming waveforms yielding discrete diffraction patterns for helical structures

    CERN Document Server

    Friesecke, Gero; Jüstel, Dominik

    2015-01-01

    Conventional X-ray methods use incoming plane waves and result in discrete diffraction patterns when scattered at crystals. Here we find, by a systematic method, incoming waveforms which exhibit discrete diffraction patterns when scattered at helical structures. As examples we present simulated diffraction patterns of carbon nanotubes and tobacco mosaic virus. The new incoming waveforms, which we call twisted waves due to their geometric shape, are found theoretically as closed-form solutions to Maxwell's equations. The theory of the ensuing diffraction patterns is developed in detail. A twisted analogue of the Von Laue condition is seen to hold, with the peak locations encoding the symmetry and the helix parameters, and the peak intensities indicating the electronic structure in the unit cell. If suitable twisted X-ray sources can in the future be realized experimentally, it appears from our mathematical results that they will provide a powerful tool for directly determining the detailed atomic structure of ...

  11. 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

  12. 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.

  13. 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.

  14. 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

  15. Kinetics and mechanism of the barotropic lamellar gel/lamellar liquid crystal phase transition in fully hydrated dihexadecylphosphatidylethanolamine: a time-resolved x-ray diffraction study using pressure jump.

    Science.gov (United States)

    Cheng, A; Hummel, B; Mencke, A; Caffrey, M

    1994-07-01

    The kinetics and mechanism of the barotropic lamellar gel (L beta')/lamellar liquid crystal (L alpha) phase transition in fully hydrated 1,2-dihexadecyl-sn-glycero-3-phosphoethanolamine (DHPE) has been studied using time-resolved x-ray diffraction (TRXRD). The phase transition was induced by pressure jumps of varying amplitudes in both the pressurization and depressurization directions at controlled temperature (78 degrees C). Both low- and wide-angle diffracted x rays were recorded simultaneously in live time using an x-ray-sensitive image intensifier coupled to a CCD camera and Super-VHS videotape recorder. Such an arrangement allowed for the direct and quantitative characterization of the long- (lamellar repeat spacing) and short-range order (chain packing) during a kinetic experiment. The image-processed live-time x-ray diffraction data were fitted using a nonlinear least-squares model, and the parameters of the fits were monitored continuously throughout the transition. The pressure-induced transitions from the L alpha to the L beta' phase and from the L beta' to the L alpha phase was two-state (no formation of intermediates apparent during the transition) to within the sensitivity limits of the method. The corresponding transit time (the time during which both phases coexist) associated with the long- and short-range order of the pressurization-induced L alpha-to-L beta' phase transition decreased to a limiting value of approximately 50 ms with increasing pressure jump amplitude. This limiting value was close to the response time of the detector/recording system. Thus, the intrinsic transit time of this transition in fully hydrated DHPE at 78 degrees C was less than or equal to 50 ms. In contrast, the depressurization-induced L beta'-to-L alpha phase transition was slower, taking approximately 1 s to complete, and occurred with no obvious dependence of the transit time on pressure jump amplitude. In the depressurization jump experiment, the lipid responded

  16. X-ray Diffraction Study of Arsenopyrite at High Pressure

    Energy Technology Data Exchange (ETDEWEB)

    D Fan; M Ma; W Zhou; S Wei; Z Chen; H Xie

    2011-12-31

    The high-pressure X-ray diffraction study of a natural arsenopyrite was investigated up to 28.2 GPa using in situ angle-dispersive X-ray diffraction and a diamond anvil cell at National Synchrotron Light Source, Brookhaven National Laboratory. The 16:3:1 methanol-ethanol-water mixture was used as a pressure-transmitting medium. Pressures were measured using the ruby-fluorescence method. No phase change has been observed up to 28.2 GPa. The isothermal equation of state (EOS) was determined. The values of K{sub 0}, and K'{sub 0} refined with a third-order Birch-Murnaghan EOS are K{sub 0} = 123(9) GPa, and K'{sub 0} = 5.2(8). Furthermore, we confirm that the linear compressibilities ({beta}) along a, b and c directions of arsenopyrite is elastically isotropic ({beta}{sub a} = 6.82 x 10{sup -4}, {beta}{sub b} = 6.17 x 10{sup -4} and {beta}{sub c} = 6.57 x 10{sup -4} GPa{sup -1}).

  17. X-ray diffraction study of arsenopyrite at high pressure

    Science.gov (United States)

    Fan, D. W.; Ma, M. N.; Zhou, W. G.; Wei, S. Y.; Chen, Z. Q.; Xie, H. S.

    2011-02-01

    The high-pressure X-ray diffraction study of a natural arsenopyrite was investigated up to 28.2 GPa using in situ angle-dispersive X-ray diffraction and a diamond anvil cell at National Synchrotron Light Source, Brookhaven National Laboratory. The 16:3:1 methanol-ethanol-water mixture was used as a pressure-transmitting medium. Pressures were measured using the ruby-fluorescence method. No phase change has been observed up to 28.2 GPa. The isothermal equation of state (EOS) was determined. The values of K 0, and K' 0 refined with a third-order Birch-Murnaghan EOS are K 0 = 123(9) GPa, and K' 0 = 5.2(8). Furthermore, we confirm that the linear compressibilities (β) along a, b and c directions of arsenopyrite is elastically isotropic (β a = 6.82 × 10-4, β b = 6.17 × 10-4 and β c = 6.57 × 10-4 GPa-1).

  18. Characterization of Brazilian asphalt using X-ray diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Cardoso, Edson R.; Pinto, Nivia G.V.; Almeida, Ana P.G.; Braz, Delson; Lopes, Ricardo T. [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Coordenacao dos Programas de Pos-graduacao de Engenharia (COPPE). Lab. de Instrumentacao Nuclear], E-mail: ecardoso@lin.ufrj.br; Barroso, Regina C. [Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, RJ (Brazil). Inst. de Fisica], E-mail: cely@uerj.br; Motta, Laura M.G. [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Coordenacao dos Programas de Pos-graduacao de Engenharia (COPPE). Lab. de Geotecnia], E-mail: laura@coc.ufrj.br

    2007-07-01

    Asphalt is a sticky, black and highly viscous liquid or semi-solid that is presented in most crude petroleum and in some natural deposits. The X ray diffraction can give valuable information over the characteristics of a material. Thus, the X-ray diffraction (XRD) method was employed to investigate parameters that characterize and differentiate asphalt groups (Boscan, CAP20, CAP40, CAP50/60, CAP50/70 and CAP85/100). The scattering measurements were carried out in {theta}-2{theta} reflection geometry using a powder diffractometer Shimadzu XRD-6000 at the Nuclear Instrumentation Laboratory, Brazil. Scans were typically done from 8 deg to 28 deg every 0.05. The parameters analyzed were: FWHM, peak area, peak center, peak height, left half width and right half width. Thus, in this study, scattering profiles from different asphalt groups were carefully measured in order to establish characteristic signatures of these materials. The results indicate that by using three parameters (peak centroid, peak area and peak intensity) it is possible to characterize and differentiate the asphalt. (author)

  19. X-ray diffraction of III-nitrides

    Energy Technology Data Exchange (ETDEWEB)

    Moram, M A; Vickers, M E [Department of Materials Science and Metallurgy, University of Cambridge, Pembroke St., Cambridge, CB2 3QZ (United Kingdom)], E-mail: mam65@cam.ac.uk

    2009-03-15

    The III-nitrides include the semiconductors AlN, GaN and InN, which have band gaps spanning the entire UV and visible ranges. Thin films of III-nitrides are used to make UV, violet, blue and green light-emitting diodes and lasers, as well as solar cells, high-electron mobility transistors (HEMTs) and other devices. However, the film growth process gives rise to unusually high strain and high defect densities, which can affect the device performance. X-ray diffraction is a popular, non-destructive technique used to characterize films and device structures, allowing improvements in device efficiencies to be made. It provides information on crystalline lattice parameters (from which strain and composition are determined), misorientation (from which defect types and densities may be deduced), crystallite size and microstrain, wafer bowing, residual stress, alloy ordering, phase separation (if present) along with film thicknesses and superlattice (quantum well) thicknesses, compositions and non-uniformities. These topics are reviewed, along with the basic principles of x-ray diffraction of thin films and areas of special current interest, such as analysis of non-polar, semipolar and cubic III-nitrides. A summary of useful values needed in calculations, including elastic constants and lattice parameters, is also given. Such topics are also likely to be relevant to other highly lattice-mismatched wurtzite-structure materials such as heteroepitaxial ZnO and ZnSe.

  20. X-ray diffraction of III-nitrides

    Science.gov (United States)

    Moram, M A; Vickers, M E

    2009-03-01

    The III-nitrides include the semiconductors AlN, GaN and InN, which have band gaps spanning the entire UV and visible ranges. Thin films of III-nitrides are used to make UV, violet, blue and green light-emitting diodes and lasers, as well as solar cells, high-electron mobility transistors (HEMTs) and other devices. However, the film growth process gives rise to unusually high strain and high defect densities, which can affect the device performance. X-ray diffraction is a popular, non-destructive technique used to characterize films and device structures, allowing improvements in device efficiencies to be made. It provides information on crystalline lattice parameters (from which strain and composition are determined), misorientation (from which defect types and densities may be deduced), crystallite size and microstrain, wafer bowing, residual stress, alloy ordering, phase separation (if present) along with film thicknesses and superlattice (quantum well) thicknesses, compositions and non-uniformities. These topics are reviewed, along with the basic principles of x-ray diffraction of thin films and areas of special current interest, such as analysis of non-polar, semipolar and cubic III-nitrides. A summary of useful values needed in calculations, including elastic constants and lattice parameters, is also given. Such topics are also likely to be relevant to other highly lattice-mismatched wurtzite-structure materials such as heteroepitaxial ZnO and ZnSe.