Facile synthesis, single crystal analysis, and computational studies of sulfanilamide derivatives

Science.gov (United States)

Tahir, Muhammad Nawaz; Khalid, Muhammad; Islam, Ayesha; Ali Mashhadi, Syed Muddassir; Braga, Ataualpa A. C.

2017-01-01

Antibacterial resistance is a worldwide problem. Sulfanilamide is widely used antibacterial. For the first time, we report here a simple method for the derivative synthesis of the title drugs, single crystal XRD and density functional theory (DFT) studies. The optimized molecular structure, natural bond orbital (NBO), frontier molecular orbitals (FMOs) molecular electrostatic potential studies (MEP) and Mulliken population analysis (MPA) have been performed using M06-2X/6-31G(d, p). The FT-IR spectra and thermodynamic parameters were calculated at M06-2X/6-311 + G(2d,p) and B3LYP/6-31G(d, p) levels respectively, while, the UV-Vis analysis was performed using TD-DFT/B3LYP/6-31G(d, p) method. The experimental FT-IR spectra of both compounds were also carried out to reconfirm sbnd H⋯Osbnd hydrogen bonds. The DFT optimized parameters exhibiting good agreement with the experimental data. NBO analysis explored the hyper conjugative interaction and stability of title crystals, especially, reconfirmed the existence of sbnd H⋯Osbnd hydrogen bonds between the dimers. The FT-IR, thermodynamic parameters, MEP and MPA also revealed the hydrogen bonding detail is harmonious to XRD data. As a matter of the fact, the hydrogen bonding is a significant parameter for the understanding and design of molecular crystals, subsequently; it can also play a vital role in the supramolecular chemistry. Moreover, the global reactivity descriptors suggest that title compounds might be bioactive.

Convergence of surface diffusion parameters with model crystal size

Science.gov (United States)

Cohen, Jennifer M.; Voter, Arthur F.

1994-07-01

A study of the variation in the calculated quantities for adatom diffusion with respect to the size of the model crystal is presented. The reported quantities include surface diffusion barrier heights, pre-exponential factors, and dynamical correction factors. Embedded atom method (EAM) potentials were used throughout this effort. Both the layer size and the depth of the crystal were found to influence the values of the Arrhenius factors significantly. In particular, exchange type mechanisms required a significantly larger model than standard hopping mechanisms to determine adatom diffusion barriers of equivalent accuracy. The dynamical events that govern the corrections to transition state theory (TST) did not appear to be as sensitive to crystal depth. Suitable criteria for the convergence of the diffusion parameters with regard to the rate properties are illustrated.

Crystallization and preliminary X-ray diffraction analysis of rat autotaxin

International Nuclear Information System (INIS)

Day, Jacqueline E.; Hall, Troii; Pegg, Lyle E.; Benson, Timothy E.; Hausmann, Jens; Kamtekar, Satwik

2010-01-01

Autotaxin (ATX), a pyrophosphatase/phosphodiesterase enzyme, is a promising drug target for many indications and is only distantly related to enzymes of previously determined structure. Here, the cloning, expression, purification, crystallization and preliminary diffraction analysis of ATX are reported. Rat autotaxin has been cloned, expressed, purified to homogeneity and crystallized via hanging-drop vapour diffusion using PEG 3350 as precipitant and ammonium iodide and sodium thiocyanate as salts. The crystals diffracted to a maximum resolution of 2.05 Å and belonged to space group P1, with unit-cell parameters a = 53.8, b = 63.3, c = 70.5 Å, α = 98.8, β = 106.2, γ = 99.8°. Preliminary X-ray diffraction analysis indicated the presence of one molecule per asymmetric unit, with a solvent content of 47%

Q-space analysis of light scattering by ice crystals

Science.gov (United States)

Heinson, Yuli W.; Maughan, Justin B.; Ding, Jiachen; Chakrabarti, Amitabha; Yang, Ping; Sorensen, Christopher M.

2016-12-01

Q-space analysis is applied to extensive simulations of the single-scattering properties of ice crystals with various habits/shapes over a range of sizes. The analysis uncovers features common to all the shapes: a forward scattering regime with intensity quantitatively related to the Rayleigh scattering by the particle and the internal coupling parameter, followed by a Guinier regime dependent upon the particle size, a complex power law regime with incipient two dimensional diffraction effects, and, in some cases, an enhanced backscattering regime. The effects of significant absorption on the scattering profile are also studied. The overall features found for the ice crystals are similar to features in scattering from same sized spheres.

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

International Nuclear Information System (INIS)

Kaufmann, Bärbel; Plevka, Pavel; Kuhn, Richard J.; Rossmann, Michael G.

2010-01-01

Crystals of infectious West Nile virus were obtained and diffracted at best to about 25 Å resolution. Preliminary analysis of the diffraction pattern suggested tight hexagonal packing of the intact virus. 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 Å using synchrotron radiation. A preliminary analysis of the diffraction images indicated that the crystals had unit-cell parameters a ≃ b ≃ 480 Å, γ = 120°, suggesting a tight hexagonal packing of one virus particle per unit cell

Improved reproducibility of unit-cell parameters in macromolecular cryocrystallography by limiting dehydration during crystal mounting.

Science.gov (United States)

Farley, Christopher; Burks, Geoffry; Siegert, Thomas; Juers, Douglas H

2014-08-01

In macromolecular cryocrystallography unit-cell parameters can have low reproducibility, limiting the effectiveness of combining data sets from multiple crystals and inhibiting the development of defined repeatable cooling protocols. Here, potential sources of unit-cell variation are investigated and crystal dehydration during loop-mounting is found to be an important factor. The amount of water lost by the unit cell depends on the crystal size, the loop size, the ambient relative humidity and the transfer distance to the cooling medium. To limit water loss during crystal mounting, a threefold strategy has been implemented. Firstly, crystal manipulations are performed in a humid environment similar to the humidity of the crystal-growth or soaking solution. Secondly, the looped crystal is transferred to a vial containing a small amount of the crystal soaking solution. Upon loop transfer, the vial is sealed, which allows transport of the crystal at its equilibrated humidity. Thirdly, the crystal loop is directly mounted from the vial into the cold gas stream. This strategy minimizes the exposure of the crystal to relatively low humidity ambient air, improves the reproducibility of low-temperature unit-cell parameters and offers some new approaches to crystal handling and cryoprotection.

Production, crystallization and preliminary X-ray diffraction analysis of the allergen Can f 2 from Canis familiaris

International Nuclear Information System (INIS)

Madhurantakam, Chaithanya; Nilsson, Ola B.; Jönsson, Klas; Grönlund, Hans; Achour, Adnane

2009-01-01

The recombinant form of the allergen Can f 2 from C. familiaris was produced, isolated and crystallized in two different forms. Preliminary X-ray diffraction analyses are reported for the two crystal forms of Can f 2. The allergen Can f 2 from dog (Canis familiaris) present in saliva, dander and fur is an important cause of allergic sensitization worldwide. Here, the production, isolation, crystallization and preliminary X-ray diffraction analysis of two crystal forms of recombinant Can f 2 are reported. The first crystal form belonged to space group C222, with unit-cell parameters a = 68.7, b = 77.3, c = 65.1 Å, and diffracted to 1.55 Å resolution, while the second crystal form belonged to space group C2, with unit-cell parameters a = 75.7, b = 48.3, c = 68.7 Å, β = 126.5°, and diffracted to 2.1 Å resolution. Preliminary data analysis indicated the presence of a single molecule in the asymmetric unit for both crystal forms

Calculations of the electronic levels, spin-Hamiltonian parameters and vibrational spectra for the CrCl{sub 3} layered crystals

Energy Technology Data Exchange (ETDEWEB)

Avram, C.N. [Faculty of Physics, West University of Timisoara, Bd. V. Parvan No. 4, 300223 Timisoara (Romania); Gruia, A.S., E-mail: adigruia@yahoo.com [Faculty of Physics, West University of Timisoara, Bd. V. Parvan No. 4, 300223 Timisoara (Romania); Brik, M.G. [College of Sciences, Chongqing University of Posts and Telecommunications, Chongqing 400065 (China); Institute of Physics, University of Tartu, Ravila 14C, Tartu 50411 (Estonia); Institute of Physics, Jan Dlugosz University, Armii Krajowej 13/15, PL-42200 Czestochowa (Poland); Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw (Poland); Barb, A.M. [Faculty of Physics, West University of Timisoara, Bd. V. Parvan No. 4, 300223 Timisoara (Romania)

2015-12-01

Calculations of the Cr{sup 3+} energy levels, spin-Hamiltonian parameters and vibrational spectra for the layered CrCl{sub 3} crystals are reported for the first time. The crystal field parameters and the energy level scheme were calculated in the framework of the Exchange Charge Model of crystal field. The spin-Hamiltonian parameters (zero-field splitting parameter D and g-factors) for Cr{sup 3+} ion in CrCl{sub 3} crystals were obtained using two independent techniques: i) semi-empirical crystal field theory and ii) density functional theory (DFT)-based model. In the first approach, the spin-Hamiltonian parameters were calculated from the perturbation theory method and the complete diagonalization (of energy matrix) method. The infrared (IR) and Raman frequencies were calculated for both experimental and fully optimized geometry of the crystal structure, using CRYSTAL09 software. The obtained results are discussed and compared with the experimental available data.

Cloning, expression, purification, crystallization and preliminary X-ray analysis of the pilus-associated sortase C from Streptococcus pneumoniae

International Nuclear Information System (INIS)

Neiers, F.; Madhurantakam, C.; Fälker, S.; Normark, S.; Henriques-Normark, B.; Achour, A.

2008-01-01

Crystallization conditions and preliminary X-ray diffraction analysis of the S. pneumoniae-derived pilus-associated protein sortase C are reported. The pilus-associated sortase C from Streptococcus pneumoniae (SrtC or Srt-2) acts as a polymerase for the pilus subunit proteins RrgA and RrgB. Here, the crystallization and preliminary X-ray diffraction analysis of three crystal forms of SrtC are reported. One crystal form belongs to space group P2 1 2 1 2 1 , with unit-cell parameters a = 48.9, b = 96.9, c = 98.9 Å, α = β = γ = 90°. The other two crystal forms belong to space group P222, with unit-cell parameters a = 48.8, b = 97.2, c = 99.2 Å, α = β = γ = 90° and a = 48.6, b = 96.5, c = 98.8 Å, α = β = γ = 90°, respectively. Preliminary analysis indicates the presence of two molecules in the asymmetric unit of the crystal for all three forms

Theoretical explanation of EPR parameters for Cu2+ ion in TiO2 crystal

International Nuclear Information System (INIS)

Dong, H.N.; Wu, S.Y.; Li, P.

2004-01-01

The EPR parameters anisotropic g-factors g x , g y and g z for Cu 2+ ion and hyperfine structure constants A x , A y and A z for 63 Cu 2+ and 65 Cu 2+ isotopes in rutile (TiO 2 ) crystal are calculated by the method of diagonalizing the full Hamiltonian matrix. The crystal-field parameters contact with the crystal structure by the aid of the superposition model. The calculated results are in reasonable agreement with the observed values. The results are discussed. (copyright 2004 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

Expression, purification, crystallization and preliminary X-ray analysis of Aeromonas hydrophilia metallo-β-lactamase

Energy Technology Data Exchange (ETDEWEB)

Sharma, Nandini, E-mail: nandini-sharma@merck.com; Toney, Jeffrey H.; Fitzgerald, Paula M. D.

2005-02-01

Crystallization and preliminary X-ray analysis of the CphA metallo-β-lactamase from A. hydrophilia are described. The crystals belonged to space group P2{sub 1}2{sub 1}2, with unit-cell parameters a = 40.75, b = 42.05, c = 128.88 Å, and diffract to 1.8 Å.

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

International Nuclear Information System (INIS)

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

2010-01-01

Virions of red clover necrotic mosaic virus have been purified and crystallized. The space group was determined to be I23, with unit-cell parameter a = 377.8 Å. The crystals diffracted to 4 Å resolution. 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 Å resolution but were very radiation-sensitive, causing rapid decay of the high-resolution reflections. The data were processed to 6 Å in the analysis presented here

Modeling local structure using crystal field and spin Hamiltonian parameters: the tetragonal FeK3+-OI2- defect center in KTaO3 crystal

International Nuclear Information System (INIS)

Gnutek, P; Rudowicz, C; Yang, Z Y

2009-01-01

The local structure and the spin Hamiltonian (SH) parameters, including the zero-field-splitting (ZFS) parameters D and (a+2F/3), and the Zeeman g factors g || and g perpendicular , are theoretically investigated for the Fe K 3+ -O I 2- center in KTaO 3 crystal. The microscopic SH (MSH) parameters are modeled within the framework of the crystal field (CF) theory employing the CF analysis (CFA) package, which also incorporates the MSH modules. Our approach takes into account the spin-orbit interaction as well as the spin-spin and spin-other-orbit interactions omitted in previous studies. The superposition model (SPM) calculations are carried out to provide input CF parameters for the CFA/MSH package. The combined SPM-CFA/MSH approach is used to consider various structural models for the Fe K 3+ -O I 2- defect center in KTaO 3 . This modeling reveals that the off-center displacement of the Fe 3+ ions, Δ 1 (Fe 3+ ), combined with an inward relaxation of the nearest oxygen ligands, Δ 2 (O 2- ), and the existence of the interstitial oxygen O I 2- give rise to a strong tetragonal crystal field. This finding may explain the large ZFS experimentally observed for the Fe K 3+ -O I 2- center in KTaO 3 . Matching the theoretical MSH predictions with the available structural data as well as electron magnetic resonance (EMR) and optical spectroscopy data enables predicting reasonable ranges of values of Δ 1 (Fe 3+ ) and Δ 2 (O 2- ) as well as the possible location of O I 2- ligands around Fe 3+ ions in KTaO 3 . The defect structure model obtained using the SPM-CFA/MSH approach reproduces very well the ranges of the experimental SH parameters D, g || and g perpendicular and importantly yields not only the correct magnitude of D but also the sign, unlike previous studies. More reliable predictions may be achieved when experimental data on (a+2F/3) and/or crystal field energy levels become available. Comparison of our results with those arising from alternative models existing

Lidar inelastic multiple-scattering parameters of cirrus particle ensembles determined with geometrical-optics crystal phase functions.

Science.gov (United States)

Reichardt, J; Hess, M; Macke, A

2000-04-20

Multiple-scattering correction factors for cirrus particle extinction coefficients measured with Raman and high spectral resolution lidars are calculated with a radiative-transfer model. Cirrus particle-ensemble phase functions are computed from single-crystal phase functions derived in a geometrical-optics approximation. Seven crystal types are considered. In cirrus clouds with height-independent particle extinction coefficients the general pattern of the multiple-scattering parameters has a steep onset at cloud base with values of 0.5-0.7 followed by a gradual and monotonic decrease to 0.1-0.2 at cloud top. The larger the scattering particles are, the more gradual is the rate of decrease. Multiple-scattering parameters of complex crystals and of imperfect hexagonal columns and plates can be well approximated by those of projected-area equivalent ice spheres, whereas perfect hexagonal crystals show values as much as 70% higher than those of spheres. The dependencies of the multiple-scattering parameters on cirrus particle spectrum, base height, and geometric depth and on the lidar parameters laser wavelength and receiver field of view, are discussed, and a set of multiple-scattering parameter profiles for the correction of extinction measurements in homogeneous cirrus is provided.

Studying The Effect of Various Parameters on The Characteristics of The Dielectric and Metallic Photonic Crystals

International Nuclear Information System (INIS)

Ismail, M.; Badawy, Z.M.; Abdel-Rahman, E.

2015-01-01

Transmittance characteristics of two types of photonic crystals have been analysed using the transfer matrix method. The first one is the dielectric photonic crystal (DPC), and the second is the metallic photonic crystal (MPC). The effect of the most parameters on the transmission spectra of the dielectric and metallic photonic crystals has been studied

Theoretical calculations of spin-Hamiltonian parameters for the rhombic-like Mo5+ centers in KTiOPO4 crystal

International Nuclear Information System (INIS)

Yang, Mei; Wen-Chen, Zheng; Hong-Gang, Liu

2013-01-01

The spin-Hamiltonian parameters (g factors g i and hyperfine structure constants A i , were i=x, y and z) for Mo 5+ ion occupying the Ti(1) site with approximately rhombic symmetry in KTiOPO 4 crystal are calculated from the high-order perturbation formulas based on the two-mechanism model. In the model, not only the contribution due to the conventional crystal-field (CF) mechanism, but also those due to the charge-transfer (CT) mechanism are included. The six calculated spin-Hamiltonian parameters with four adjustable parameters are in reasonable agreement with the experimental values. The calculations show that for more accurate calculations of spin-Hamiltonian parameters of the high valence d n ions (e.g., Mo 5+ considered here) in crystals, the contribution from CT mechanism, which is ignored in the conventional crystal field theory, should be taken into account. The reasonable crystal field energy levels of Mo 5+ in KTiOPO 4 are also predicted from calculations

Crystallization and preliminary X-ray analysis of pyruvate kinase from Bacillus stearothermophilus

International Nuclear Information System (INIS)

Suzuki, Kenichiro; Ito, Sohei; Shimizu-Ibuka, Akiko; Sakai, Hiroshi

2005-01-01

This report describes the crystallization and X-ray diffraction data collection of three types (wild-type, W416F/V435W and C9S/C268S) of B. stearothermophilus. Crystals of C9S/C268S belonged to space group P6 2 22 and diffracted to a resolution of 2.4 Å. Pyruvate kinase (PK) from a moderate thermophile, Bacillus stearothermophilus (BstPK), is an allosteric enzyme activated by AMP and ribose 5-phosphate but not by fructose 1,6-bisphosphate (FBP). However, almost all other PKs are activated by FBP. The wild-type and W416F/V435W mutant BstPKs were crystallized by the hanging-drop vapour-diffusion method. However, they were unsuitable for structural analysis because their data sets exhibited low completeness. A crystal suitable for structural analysis was obtained using C9S/C268S enzyme. The crystal belonged to space group P6 2 22, with unit-cell parameters a = b = 145.97, c = 118.03 Å

Crystallization and preliminary X-ray analysis of Escherichia coli RNase G

International Nuclear Information System (INIS)

Fang, Pengfei; Wang, Jing; Li, Xu; Guo, Min; Xing, Li; Cao, Xu; Zhu, Yi; Gao, Yan; Niu, Liwen; Teng, Maikun

2009-01-01

Full-length E. coli RNase G was overexpressed, purified and crystallized. Diffraction data were collected to a resolution of 3.4 Å. The homologous RNases RNase E and RNase G are widely distributed in bacteria and function in many important physiological processes, including mRNA degradation, rRNA maturation and so on. In this study, the crystallization and preliminary X-ray analysis of RNase G from Escherichia coli is described. Purified recombinant E. coli RNase G, which has 497 amino acids, was crystallized in the cubic space group F432, with unit-cell parameters a = b = c = 219.84 Å. X-ray diffraction data were collected to a resolution of 3.4 Å

Comparison of functional parameters of CsI:Tl crystals and thick films

International Nuclear Information System (INIS)

Fedorov, A.; Gektin, A.; Lebedynskiy, A.; Mateychenko, P.; Shkoropatenko, A.

2013-01-01

500 mkm thick CsI:Tl columnar films can be produced using thermal evaporation in vacuum by sublimation of the same bulk crystal. Comparison of afterglow and radiation stability of deposited CsI:Tl films with source crystal was the aim of current work. It is shown that the afterglow in the films is always below its level in initial single crystal. It was ascertained that the annealing atmospheres influence the processes leading to the activator depletion of the films during the thermal processing. -- Highlights: ► Thick CsI:Tl columnar films were obtained by thermal evaporation in vacuum. ► Radiation stability of such CsI:Tl films appears to be better than that of crystal. ► CsI:Tl film parameters can be modified by annealing in different atmospheres

Off-line analysis of positron annihilation spectra. II. Defining crystal frame origin

International Nuclear Information System (INIS)

Adam, Gh.; Adam, S.

1997-01-01

This paper is devoted to the consistent definition of the origin Γ of the crystal frame (CF) of an n-axis-projected histogram (where n-vector denotes a principal crystallographic axis) obtained by the technique of the two dimensional angular correlation of positron-electron annihilation radiation (2D-ACAR). This is shown to need agreement with each other of two alternative definitions of Γ as center of symmetry and center of gravity of areas entering the signature of crystal symmetry (SCS) of the spectrum defined in a previous paper. This requirement singles out the projection of the first Brillouin zone onto the histogram plane as the area containing the information which is the least distorted by the instrumental artifacts. The derivation of Γ involves two steps described in Section 2 and 3, respectively. Consistency with each other of the obtained solutions provides a first family of validation tests. The CF validation is to be decided from the analysis of the artifact distribution in the Cf histogram. The histogram reformulation in the crystal frame is legitimate provided the Euler angle θ relating the crystal and laboratory frames is negligible . Among the criteria for the validation of the analysis of primary importance is the requirement of close agreement between the two alternative definitions of the zero-momentum projection of the momentum distribution onto the histogram plane. The histogram redefinition in the crystal frame results in specific discretization errors. To check there magnitude the SCS values are computed again and the derivation CF parameters repeated the convergence of this iterative refinement of the CF parameters offers a supplementary insight into the crystal-detector alignment and crystal quality. The described procedure is applied to three 2D-ACAR histograms

Efficient green luminescence of terbium oxalate crystals: A case study with Judd-Ofelt theory and single crystal structure analysis and the effect of dehydration on luminescence

Science.gov (United States)

Alexander, Dinu; Joy, Monu; Thomas, Kukku; Sisira, S.; Biju, P. R.; Unnikrishnan, N. V.; Sudarsanakumar, C.; Ittyachen, M. A.; Joseph, Cyriac

2018-06-01

Design and synthesis of Lanthanide based metal organic framework is a frontier area of research owing to their structural diversity enabling specific applications. The luminescence properties of rare earths, tuned by the structural features of Ln-MOFs are investigated extensively. Rare earth oxalates which can be synthesized in a facile method, ensuring the structural features of MOFs with excellent photoluminescence characteristics deserves much attention. This work is the first time report on the single crystal structure and Judd-Ofelt (JO) theoretical analysis - their correlation with the intense and sharp green luminescence of Terbium oxalate crystals. The intense green luminescence observed for Terbium oxalate crystals for a wide range of excitation from DUV to visible region despite the luminescence limiting factors are discussed. The absence of concentration quenching and lifting up of forbidden nature of f-f transitions, allowing direct excitation of Terbium ions is analysed with the help of JO theory and single crystal structure analysis. The JO analysis predicted the asymmetry of Terbium sites, allowing the electric dipole transitions and from the JO intensity parameters, promising spectroscopic parameters - emission cross section, branching ratio, gain band width and gain coefficient of the material were calculated. The single crystal structure analysis revealed the asymmetry of Tb sites and structure of Terbium oxalate is formed by the hydrogen bonded stacking of overlapped six Terbium membered rings connected by the oxalate ligands. The molecularly thick layers thus formed on the crystal surface are imaged by the atomic force microscopy. The presence of water channels in the structure and the effect of lattice water molecules on the luminescence intensity are also investigated.

Effect of processing parameters of rotary ultrasonic machining on surface integrity of potassium dihydrogen phosphate crystals

Directory of Open Access Journals (Sweden)

Jianfu Zhang

2015-09-01

Full Text Available Potassium dihydrogen phosphate is an important optical crystal. However, high-precision processing of large potassium dihydrogen phosphate crystal workpieces is difficult. In this article, surface roughness and subsurface damage characteristics of a (001 potassium dihydrogen phosphate crystal surface produced by traditional and rotary ultrasonic machining are studied. The influence of process parameters, including spindle speed, feed speed, type and size of sintered diamond wheel, ultrasonic power, and selection of cutting fluid on potassium dihydrogen phosphate crystal surface integrity, was analyzed. The surface integrity, especially the subsurface damage depth, was affected significantly by the ultrasonic power. Metal-sintered diamond tools with high granularity were most suitable for machining potassium dihydrogen phosphate crystal. Cutting fluid played a key role in potassium dihydrogen phosphate crystal machining. A more precise surface can be obtained in machining with a higher spindle speed, lower feed speed, and using kerosene as cutting fluid. Based on the provided optimized process parameters for machining potassium dihydrogen phosphate crystal, a processed surface quality with Ra value of 33 nm and subsurface damage depth value of 6.38 μm was achieved.

Crystallization and preliminary X-ray analysis of S-ribosylhomocysteinase from Streptococcus mutans

International Nuclear Information System (INIS)

Li, Hui; Zhao, Hongyan; Zhu, Laikuan; Hong, Lihua; Zhang, Hong; Lin, Fanjing; Xu, Chunyan; Li, Shentao; Zhang, Zhimin

2012-01-01

S-Ribosylhomocysteinase (LuxS) encoded by the LuxS gene from Streptococcus mutans was solubly expressed in Escherichia coli, purified and crystallized. Diffraction by the crystal extended to 2.4 Å resolution. S-Ribosylhomocysteinase (LuxS) encoded by the luxS gene from Streptococcus mutans plays a crucial role in the quorum-sensing system. LuxS was solubly expressed in Escherichia coli with high yield. The purity of the purified target protein, which was identified by SDS–PAGE and MALDI–TOF MS analysis, was >95%. The protein was crystallized using the hanging-drop vapour-diffusion method with PEG 3350 as the primary precipitant. X-ray diffraction data were collected at Beijing Synchrotron Radiation Facility (BSRF). Diffraction by the crystal extended to 2.4 Å resolution and the crystal belonged to space group C222 1 , with unit-cell parameters a = 55.3, b = 148.7, c = 82.8 Å

Investigations on nucleation, HRXRD, optical, piezoelectric, polarizability and Z-scan analysis of L-arginine maleate dihydrate single crystals

Science.gov (United States)

Sakthy Priya, S.; Alexandar, A.; Surendran, P.; Lakshmanan, A.; Rameshkumar, P.; Sagayaraj, P.

2017-04-01

An efficient organic nonlinear optical single crystal of L-arginine maleate dihydrate (LAMD) has been grown by slow evaporation solution technique (SEST) and slow cooling technique (SCT). The crystalline perfection of the crystal was examined using high-resolution X-ray diffractometry (HRXRD) analysis. Photoluminescence study confirmed the optical properties and defects level in the crystal lattice. Electromechanical behaviour was observed using piezoelectric co-efficient (d33) analysis. The photoconductivity analysis confirmed the negative photoconducting nature of the material. The dielectric constant and loss were measured as a function of frequency with varying temperature and vice-versa. The laser damage threshold (LDT) measurement was carried out using Nd:YAG Laser with a wavelength of 1064 nm (Focal length is 35 cm) and the obtained results showed that LDT value of the crystal is high compared to KDP crystal. The high laser damage threshold of the grown crystal makes it a potential candidate for second and higher order nonlinear optical device application. The third order nonlinear optical parameters of LAMD crystal is determined by open-aperture and closed-aperture studies using Z-scan technique. The third order linear and nonlinear optical parameters such as the nonlinear refractive index (n2), two photon absorption coefficient (β), Real part (Reχ3) and imaginary part (Imχ3) of third-order nonlinear optical susceptibility are calculated.

Theoretical explanation of EPR parameters for Cu{sup 2+} ion in TiO{sub 2} crystal

Energy Technology Data Exchange (ETDEWEB)

Dong, H.N. [Institute of Applied Physics and College of Electronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing 400065 (China); International Centre for Materials Physics, Chinese Academy of Sciences, Shenyang 110016 (China); Wu, S.Y. [International Centre for Materials Physics, Chinese Academy of Sciences, Shenyang 110016 (China); Department of Applied Physics, University of Electronic Science and Technology of China, Chengdu 610054 (China); Li, P. [Department of Physics, The University of Hong Kong, Pokfulam Road, Hong Kong (China)

2004-07-01

The EPR parameters anisotropic g-factors g{sub x}, g{sub y} and g{sub z} for Cu{sup 2+} ion and hyperfine structure constants A{sub x}, A{sub y} and A{sub z} for {sup 63}Cu{sup 2+} and {sup 65}Cu{sup 2+} isotopes in rutile (TiO{sub 2}) crystal are calculated by the method of diagonalizing the full Hamiltonian matrix. The crystal-field parameters contact with the crystal structure by the aid of the superposition model. The calculated results are in reasonable agreement with the observed values. The results are discussed. (copyright 2004 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

Recombinant ACHT1 from Arabidopsis thaliana: crystallization and X-ray crystallographic analysis.

Science.gov (United States)

Pan, Weimin; Wang, Junchao; Yang, Ye; Liu, Lin; Zhang, Min

2017-07-01

Thioredoxins (Trxs) play important roles in chloroplasts by linking photosynthetic light reactions to a series of plastid functions. They execute their function by regulating the oxidation and reduction of disulfide bonds. ACHT1 (atypical cysteine/histidine-rich Trx1) is a thylakoid-associated thioredoxin-type protein found in the Arabidopsis thaliana chloroplast. Recombinant ACHT1 protein was overexpressed in Escherichia coli, purified and crystallized by the vapour-diffusion method. The crystal diffracted to 1.7 Å resolution and a complete X-ray data set was collected. Preliminary crystallographic analysis suggested that the crystals belonged to space group C222 1 , with unit-cell parameters a = 102.7, b = 100.6, c = 92.8 Å.

Morphology and parameters of crystallization the blend PE/Epoxy/PE-co-PEG; Morfologia e parametros de cristalizacao da blenda PE/epoxi/PE-co-PEG

Energy Technology Data Exchange (ETDEWEB)

Becker, Daniela; Coelho, Luiz Antonio Ferreira; Nack, Fernanda; Silva, Bruna Louise, E-mail: dep2db@joinville.udesc.br [Universidade do Estado de Santa Catarina (UDESC), Joinville, SC (Brazil). Centro de Ciencias Tecnologicas

2014-07-01

This study aims to evaluate the morphology and crystallization parameters of high density polyethylene (HDPE) with different concentrations of epoxy (DGEBA / OTBG), and the compatibility of this system was used and the copolymer polyethylene-block-poly (ethylene glycol) (PEG-co-PE). The blends were obtained by mechanical mixing on a torque rheometer (Haake). Determined the crystallization parameters of the test matrix differential scanning calorimetry (DSC) and by X-ray diffraction (XRD). The morphology of the system was analyzed by transmission electron microscopy (TEM). It was observed by XRD analysis that the addition of compatibilizer and epoxy resins do not interfere with the crystal structure of HDPE, indicating that the increase in crystallinity associated with the crystallization kinetics. It was observed that the compatibilizing helped the adhesion, reducing the size of the dispersed phase becomes a more stable morphology and obtaining a distribution of the dispersed epoxy phase. (author)

Crystallization Kinetics within a Generic Modeling Framework

DEFF Research Database (Denmark)

Meisler, Kresten Troelstrup; von Solms, Nicolas; Gernaey, Krist V.

2014-01-01

of employing a well-structured model library for storage, use/reuse, and analysis of the kinetic models are highlighted. Examples illustrating the application of the modeling framework for kinetic model discrimination related to simulation of specific crystallization scenarios and for kinetic model parameter......A new and extended version of a generic modeling framework for analysis and design of crystallization operations is presented. The new features of this framework are described, with focus on development, implementation, identification, and analysis of crystallization kinetic models. Issues related...... to the modeling of various kinetic phenomena like nucleation, growth, agglomeration, and breakage are discussed in terms of model forms, model parameters, their availability and/or estimation, and their selection and application for specific crystallization operational scenarios under study. The advantages...

Advanced x-ray stress analysis method for a single crystal using different diffraction plane families

International Nuclear Information System (INIS)

Imafuku, Muneyuki; Suzuki, Hiroshi; Sueyoshi, Kazuyuki; Akita, Koichi; Ohya, Shin-ichi

2008-01-01

Generalized formula of the x-ray stress analysis for a single crystal with unknown stress-free lattice parameter was proposed. This method enables us to evaluate the plane stress states with any combination of diffraction planes. We can choose and combine the appropriate x-ray sources and diffraction plane families, depending on the sample orientation and the apparatus, whenever diffraction condition is satisfied. The analysis of plane stress distributions in an iron single crystal was demonstrated combining with the diffraction data for Fe{211} and Fe{310} plane families

Crystallization and preliminary X-ray diffraction analysis of mevalonate kinase from Methanosarcina mazei

International Nuclear Information System (INIS)

Zhuang, Ningning; Seo, Kyung Hye; Chen, Cong; Zhou, Jia; Kim, Seon Won; Lee, Kon Ho

2012-01-01

Recombinant mevalonate kinase from M. mazei has been crystallized. Diffraction data were collected to 2.08 Å resolution. Mevalonate kinase (MVK), which plays an important role in catalysing the biosynthesis of isoprenoid compounds derived from the mevalonate pathway, transforms mevalonate to 5-phosphomevalonate using ATP as a cofactor. Mevalonate kinase from Methanosarcina mazei (MmMVK) was expressed in Escherichia coli, purified and crystallized for structural analysis. Diffraction-quality crystals of MmMVK were obtained by the vapour-diffusion method using 0.32 M MgCl 2 , 0.08 M bis-tris pH 5.5, 16%(w/v) PEG 3350. The crystals belonged to space group P2 1 2 1 2, with unit-cell parameters a = 97.11, b = 135.92, c = 46.03 Å. Diffraction data were collected to 2.08 Å resolution

Crystallization and crystal manipulation of a steric chaperone in complex with its lipase substrate

International Nuclear Information System (INIS)

Pauwels, Kris; Loris, Remy; Vandenbussche, Guy; Ruysschaert, Jean-Marie; Wyns, Lode; Van Gelder, Patrick

2005-01-01

Crystals of the lipase of B. glumae in complex with its specific foldase were obtained in two forms. Crystallization, crystal manipulation and preliminary X-ray diffraction analysis are described. Bacterial lipases that are secreted via the type II secretion pathway require a lipase-specific foldase in order to obtain their native and biologically active conformation in the periplasmic space. The lipase–foldase complex from Burkholderia glumae (319 and 333 residues, respectively) was crystallized in two crystal forms. One crystal form belongs to space group P3 1 21 (P3 2 21), with unit-cell parameters a = b = 122.3, c = 98.2 Å. A procedure is presented which improved the diffraction of these crystals from ∼5 to 2.95 Å. For the second crystal form, which belonged to space group C2 with unit-cell parameters a = 183.0, b = 75.7, c = 116.6 Å, X-ray data were collected to 1.85 Å

Order parameters in smectic liquid crystals

International Nuclear Information System (INIS)

Beldon, Stephen M.

2001-01-01

This thesis explores some of the important mechanisms for switching in smectic liquid crystals. It is mainly concerned with the interaction of the electric field and various order parameters in smectic phases. Distortion of these order parameters and also the layer structures associated with smectics are discussed in depth. Initial work is concentrated on the electroclinic effect of commercially available FLC mixtures, where experimental results suggest the presence of non-uniformity in the molecular director profile. Two possible models are suggested assuming a variation of the order parameter θ through the cell. The first model assumes that the smectic layers remain bookshelf-like, and the second that the layers tilt in a vertical chevron structure when a cone angle is induced electroclinically or otherwise. The latter model is the first 'order parameter' model of an electric field induced vertical chevron. The presence of non-uniformity in the director profile is sensed by a method similar to wavelength extinction spectroscopy. Investigations are undertaken on racemic smectic materials with high dielectric biaxiality. Modelling of such a material reveals a new electroclinic effect which shows a discrete second order phase transition on application of a field. It is suggested that a bistable electroclinic effect stabilised with a high frequency ac field may be realised if a residual polarisation is present in the high biaxiality material, and that this might be useful in the displays industry. Experimental investigations of such a material confirm the above effects close to the smectic A-C transition. Finally a higher order smectic phase, the smectic I* phase, is considered. The distortion of the hexagonal bond orientational order is investigated experimentally during application of an electric field. The first dynamic model of the switching process is presented, showing good agreement with the experimental results. It is suggested that the bond orientational

Crystal nucleation in binary hard-sphere mixtures: the effect of order parameter on the cluster composition

NARCIS (Netherlands)

Ni, R.; Smallenburg, F.; Filion, L.C.; Dijkstra, M.

2011-01-01

We study crystal nucleation in a binary mixture of hard spheres and investigate the composition and size of the (non)critical clusters using Monte Carlo simulations. In order to study nucleation of a crystal phase in computer simulations, a one-dimensional order parameter is usually defined to

Crystallization and initial X-ray analysis of polyhydroxyalkanoate granule-associated protein from Aeromonas hydrophila

Energy Technology Data Exchange (ETDEWEB)

Zhao, Minglian; Li, Zhenguo; Zheng, Wei; Lou, Zhiyong [MOE Key Laboratory of Protein Science, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing 100084 (China); Chen, Guo-Qiang, E-mail: chengq@stu.edu.cn [MOE Key Laboratory of Protein Science, Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing 100084 (China); Multidisciplinary Research Center, Shantou University, Shantou 515063, Guangdong (China)

2006-08-01

The phasin PhaP{sub Ah} from A. hydrophila strain 4AK4 was crystallized using the hanging-drop vapour-diffusion method. Polyhydroxyalkanoate (PHA) granule-associated proteins (phasins) were discovered in PHA-accumulating bacteria. They play a crucial role as a structural protein during initial PHA-granule formation and granule growth and also serve as interfaces for granule stabilization in vivo. The phasin PhaP{sub Ah} from Aeromonas hydrophila strain 4AK4 was crystallized using the hanging-drop vapour-diffusion method. Single crystals were cryocooled for X-ray diffraction analysis. The phasin crystals belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 80.8, b = 108.9, c = 134.4 Å.

SF-FDTD analysis of a predictive physical model for parallel aligned liquid crystal devices

Science.gov (United States)

Márquez, Andrés.; Francés, Jorge; Martínez, Francisco J.; Gallego, Sergi; Alvarez, Mariela L.; Calzado, Eva M.; Pascual, Inmaculada; Beléndez, Augusto

2017-08-01

Recently we demonstrated a novel and simplified model enabling to calculate the voltage dependent retardance provided by parallel aligned liquid crystal devices (PA-LCoS) for a very wide range of incidence angles and any wavelength in the visible. To our knowledge it represents the most simplified approach still showing predictive capability. Deeper insight into the physics behind the simplified model is necessary to understand if the parameters in the model are physically meaningful. Since the PA-LCoS is a black-box where we do not have information about the physical parameters of the device, we cannot perform this kind of analysis using the experimental retardance measurements. In this work we develop realistic simulations for the non-linear tilt of the liquid crystal director across the thickness of the liquid crystal layer in the PA devices. We consider these profiles to have a sine-like shape, which is a good approximation for typical ranges of applied voltage in commercial PA-LCoS microdisplays. For these simulations we develop a rigorous method based on the split-field finite difference time domain (SF-FDTD) technique which provides realistic retardance values. These values are used as the experimental measurements to which the simplified model is fitted. From this analysis we learn that the simplified model is very robust, providing unambiguous solutions when fitting its parameters. We also learn that two of the parameters in the model are physically meaningful, proving a useful reverse-engineering approach, with predictive capability, to probe into internal characteristics of the PA-LCoS device.

Crystallization and preliminary X-ray analysis of d-2-hydroxyacid dehydrogenase from Haloferax mediterranei

International Nuclear Information System (INIS)

Domenech, J.; Baker, P. J.; Sedelnikova, S. E.; Rodgers, H. F.; Rice, D. W.; Ferrer, J.

2009-01-01

The d-2-hydroxyacid dehydrogenase from Haloferax mediterranei has been crystallized in two different forms. Diffraction data have been collected to 1.9 Å resolution for the non-productive ternary complex of the enzyme and to 2.7 Å for the selenomethionyl derivative. d-2-Hydroxyacid dehydrogenase (D2-HDH) from Haloferax mediterranei has been overexpressed in Escherichia coli, solubilized in 8 M urea and refolded by rapid dilution. The protein was purified and crystallized by the hanging-drop vapour-diffusion method using ammonium sulfate or PEG 3350 as precipitant. Two crystal forms representing the free enzyme and the nonproductive ternary complex with α-ketohexanoic acid and NAD + grew under these conditions. Crystals of form I diffracted to beyond 3.0 Å resolution and belonged to the monoclinic space group P2 1 , with unit-cell parameters a = 66.0, b = 119.6, c = 86.2 Å, β = 96.3°. Crystals of form II diffracted to beyond 2.0 Å resolution and belonged to the triclinic space group P1, with unit-cell parameters a = 66.5, b = 75.2, c = 77.6 Å, α = 109.1, β = 107.5, γ = 95.9°. The calculated values for V M and analysis of the self-rotation and self-Patterson functions suggest that the asymmetric unit in both crystal forms contains two dimers related by pseudo-translational symmetry

Experimental investigation on dependency of interparticle distance in Coulomb crystal on various parameters

OpenAIRE

Adachi, Satoshi; Takayanagi, Masahiro; 足立　聡; 高柳　昌弘

2007-01-01

Dependency of interparticle distance in Coulomb crystal on various parameters such as plasma density, electron temperature, plasma potential and the Debye length are experimentally investigated. From the investigation, it is found that the interparticle distance is proportional to the Debye length.

Crystallization of carbohydrate oxidase from Microdochium nivale

International Nuclear Information System (INIS)

Dušková, Jarmila; Dohnálek, Jan; Skálová, Tereza; Østergaard, Lars Henrik; Fuglsang, Claus Crone; Kolenko, Petr; Štěpánková, Andrea; Hašek, Jindřich

2009-01-01

Industrially used carbohydrate oxidase was successfully crystallized in several forms, diffraction data suitable for structural analysis were collected. Microdochium nivale carbohydrate oxidase was produced by heterologous recombinant expression in Aspergillus oryzae, purified and crystallized. The enzyme crystallizes with varying crystal morphologies depending on the crystallization conditions. Several different crystal forms were obtained using the hanging-drop vapour-diffusion method, two of which were used for diffraction measurements. Hexagon-shaped crystals (form I) diffracted to 2.66 Å resolution, with unit-cell parameters a = b = 55.7, c = 610.4 Å and apparent space group P6 2 22. Analysis of the data quality showed almost perfect twinning of the crystals. Attempts to solve the structure by molecular replacement did not give satisfactory results. Recently, clusters of rod-shaped crystals (form II) were grown in a solution containing PEG MME 550. These crystals belonged to the monoclinic system C2, with unit-cell parameters a = 132.9, b = 56.6, c = 86.5 Å, β = 95.7°. Data sets were collected to a resolution of 2.4 Å. The structure was solved by the molecular-replacement method. Model refinement is currently in progress

Framework for the analysis of crystallization operations

DEFF Research Database (Denmark)

Meisler, Kresten Troelstrup; Abdul Samad, Noor Asma Fazli Bin; Gernaey, Krist

Crystallization is often applied in the production of salts and/oractive pharmaceutical ingredients (API), and the crystallization step is an essential part of the manufacturing process for many chemicals-based products.In recent years the monitoring and analysis of crystallization operations has...

Crystallization and preliminary X-ray diffraction analysis of diaminopimelate epimerase from Escherichia coli

International Nuclear Information System (INIS)

Hor, Lilian; Dobson, Renwick C. J.; Dogovski, Con; Hutton, Craig A.; Perugini, Matthew A.

2009-01-01

Diaminopimelate (DAP) epimerase, an enzyme in the lysine-biosynthetic pathway, is a promising target for antibiotic development against pathogenic bacteria. Here, the cloning, expression, purification, crystallization and preliminary diffraction analysis of DAP epimerase from E. coli are reported. Diaminopimelate (DAP) epimerase (EC 5.1.1.7) catalyzes the penultimate step of lysine biosynthesis in bacteria and plants, converting l,l-diaminopimelate to meso-diaminopimelate. Here, the cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of DAP epimerase from Escherichia coli are presented. Crystals were obtained in space group P4 1 2 1 2 and diffracted to 2.0 Å resolution, with unit-cell parameters a = b = 89.4, c = 179.6 Å. Molecular replacement was conducted using Bacillus anthracis DAP epimerase as a search model and showed the presence of two molecules in the asymmetric unit, with an initial R free of 0.456 and R work of 0.416

Investigations on critical parameters, growth, structural and spectral studies of beta-alaninium picrate (BAP) single crystals

International Nuclear Information System (INIS)

Shanthi, D; Selvarajan, P; Perumal, S

2014-01-01

Beta-alaninium picrate (BAP) salt has been synthesized and the solubility of the synthesized sample in double distilled water was determined at different temperatures. Solution stability was studied by observing the metastable zone width by employing the polythermal method. Induction period values for different supersaturation ratios at room temperature were determined based on the isothermal method. The nucleation parameters such as critical radius, critical free energy change, interfacial tension, and nucleation rate have been estimated for BAP salt on the basis of the classical nucleation theory. The lattice parameters of the grown BAP crystal were determined using the x-ray diffraction (XRD) technique. The reflection planes of the sample were confirmed by the powder XRD study and diffraction peaks were indexed. Fourier transform infrared spectroscopy and Fourier transform–Raman studies were used to confirm the presence of various functional groups in the BAP crystal. The nonlinear optical property of the grown crystal was studied using the Kurtz–Perry powder technique. UV–visible spectral studies were carried out to understand optical transparency and the type of band gap of the grown BAP crystal. (paper)

Crystal-field analysis for RE3+ ions in laser materials: II. Absorption spectra and energy levels calculations for Nd3+ ions doped into SrLaGa3O7 and BaLaGa3O7 crystals and Tm3+ ions in SrGdGa3O7

International Nuclear Information System (INIS)

Karbowiak, M.; Gnutek, P.; Rudowicz, C.; Ryba-Romanowski, W.

2011-01-01

Graphical abstract: In this paper we report a detailed analysis of spectroscopic data obtained from low temperature absorption spectra, which enabled assignment of energy levels, and subsequently their analysis in terms of the free-ion and crystal field (CF) parameters. Highlights: → Polarized absorption spectra measured for Nd 3+ and Tm 3+ ions in ABC 3 O 7 crystals. → Energy levels analyzed in terms of the free-ion and crystal-field (CF) parameters. → The combined ADS/SPM procedure have been successfully applied. → The B-bar k parameters and the power law exponents t k of SPM model are determined. → The energies of levels are important for evaluation of the emission cross-section. - Abstract: Low temperature polarized absorption spectra are analyzed to achieve assignments of energy levels for Nd 3+ and Tm 3+ ions at monoclinic C s site symmetry in ABC 3 O 7 crystals. Based on the concept of average optical center, the experimental energy levels for single crystals of SrLaGa 3 O 7 :Nd 3+ (SLG:Nd), BaLaGa 3 O 7 :Nd 3+ (BLG:Nd), and SrGdGa 3 O 7 :Tm 3+ (SGG:Tm) were analyzed in terms of the free-ion parameters and the crystal field (CF) ones, B kq . Assignments of the energy levels resolved in the spectra were done in stages applying the ascent/descent in symmetry method in CF analysis. The actual monoclinic C s site symmetry at the metal centers in ABC 3 O 7 crystals and the approximated orthorhombic C 2v and tetragonal C 4v symmetry were considered. The starting values of B kq 's for SLG:Nd and BLG:Nd crystals were obtained from superposition model (SPM) analysis. The final fitted crystal field parameters show high compatibility with the existing data for structurally similar ion-host systems. The obtained values of the intrinsic parameters provide basis for SPM analysis of CF parameters for rare earth ions in other similar systems, especially those exhibiting low-symmetry sites. The SPM parameters derived for SLG:Nd are used for simulation and

Influence of Nd dopants on lattice parameters and thermal and elastic properties in YVO4 single crystals

International Nuclear Information System (INIS)

Kucytowski, J.; Wokulska, K.; Kazmierczak-Balata, A.; Bodzenta, J.; Lukasiewicz, T.; Hofman, B.; Pyka, M.

2008-01-01

The influence of neodymium doping on YVO 4 single crystals has been studied. The crystals were grown by the Czochralski method. One of them was pure YVO 4 and the others were doped with neodymium (YVO 4 :Nd) at various concentrations of Nd = 0.3-3.0 at.%. The changes of the lattice parameters were determined by the Bond's method [W.L. Bond, Acta Cryst. 13 (1960) 814]. The thermal diffusivity and the velocity of ultrasound using the photothermal method with mirage effect and the pulse echo method [J. Bodzenta, M. Pyka, J. Phys. IV France 137 (2006) 259] were measured. In the examined crystals, it was found that the lattice parameters increase while the thermal diffusivity decreases with increasing concentration of Nd atoms

Escherichia coli tRNAArg acceptor-stem isoacceptors: comparative crystallization and preliminary X-ray diffraction analysis

International Nuclear Information System (INIS)

Eichert, André; Schreiber, Angela; Fürste, Jens P.; Perbandt, Markus; Betzel, Christian; Erdmann, Volker A.; Förster, Charlotte

2009-01-01

Various E. coli tRNA Arg acceptor-stem microhelix isoacceptors have been crystallized and investigated by high-resolution X-ray diffraction analysis. The aminoacylation of tRNA is a crucial step in cellular protein biosynthesis. Recognition of the cognate tRNA by the correct aminoacyl-tRNA synthetase is ensured by tRNA identity elements. In tRNA Arg , the identity elements consist of the anticodon, parts of the D-loop and the discriminator base. The minor groove of the aminoacyl stem interacts with the arginyl-tRNA synthetase. As a consequence of the redundancy of the genetic code, six tRNA Arg isoacceptors exist. In the present work, three different Escherichia coli tRNA Arg acceptor-stem helices were crystallized. Two of them, the tRNA Arg microhelices RR-1660 and RR-1662, were examined by X-ray diffraction analysis and diffracted to 1.7 and 1.8 Å resolution, respectively. The tRNA Arg RR-1660 helix crystallized in space group P1, with unit-cell parameters a = 26.28, b = 28.92, c = 29.00 Å, α = 105.74, β = 99.01, γ = 97.44°, whereas the tRNA Arg RR-1662 helix crystallized in space group C2, with unit-cell parameters a = 33.18, b = 46.16, c = 26.04 Å, β = 101.50°

Crystallization and preliminary X-ray analysis of argininosuccinate lyase from Streptococcus mutans

International Nuclear Information System (INIS)

Cao, Yan-Li; Li, Gui-Lan; Wang, Kai-Tuo; Zhang, Hong-Yin; Li, Lan-Fen

2011-01-01

Crystals of argininosuccinate lyase from S. mutans were obtained and X-ray data were collected to 2.5 Å resolution in space group R3. Argininosuccinate lyase (ASL) is an important enzyme in arginine synthesis and the urea cycle, which are highly conserved from bacteria to eukaryotes. The gene encoding Streptococcus mutans ASL (smASL) was amplified and cloned into expression vector pET28a. The recombinant smASL protein was expressed in a soluble form in Escherichia coli strain BL21 (DE3) and purified to homogeneity by two-step column chromatography. Crystals suitable for X-ray analysis were obtained and X-ray diffraction data were collected to a resolution of 2.5 Å. The crystals belonged to space group R3, with unit-cell parameters a = b = 254.5, c = 78.3 Å

Strain gradient crystal plasticity analysis of a single crystal containing a cylindrical void

DEFF Research Database (Denmark)

Borg, Ulrik; Kysar, J.W.

2007-01-01

to one another. Finite element simulations are performed using a strain gradient crystal plasticity formulation with an intrinsic length scale parameter in a non-local strain gradient constitutive framework. For a vanishing length scale parameter the non-local formulation reduces to a local crystal...... plasticity formulation. The stress and deformation fields obtained with a local non-hardening constitutive formulation are compared to those obtained from a local hardening formulation and to those from a non-local formulation. Compared to the case of the non-hardening local constitutive formulation......, it is shown that a local theory with hardening has only minor effects on the deformation field around the void, whereas a significant difference is obtained with the non-local constitutive relation. Finally, it is shown that the applied stress state required to activate plastic deformation at the void is up...

Temperature sensitivity of void nucleation and growth parameters for single crystal copper: a molecular dynamics study

International Nuclear Information System (INIS)

Rawat, S; Chavan, V M; Warrier, M; Chaturvedi, S

2011-01-01

The effect of temperature on the void nucleation and growth is studied using the molecular dynamics (MD) code LAMMPS (Large-Scale Atomic/Molecular Massively Parallel Simulator). Single crystal copper is triaxially expanded at 5 × 10 9  s −1 strain rate keeping the temperature constant. It is shown that the nucleation and growth of voids at these atomistic scales follows a macroscopic nucleation and growth (NAG) model. As the temperature increases there is a steady decrease in the nucleation and growth thresholds. As the melting point of copper is approached, a double-dip in the pressure–time profile is observed. Analysis of this double-dip shows that the first minimum corresponds to the disappearance of the long-range order due to the creation of stacking faults and the system no longer has a FCC structure. There is no nucleation of voids at this juncture. The second minimum corresponds to the nucleation and incipient growth of voids. We present the sensitivity of NAG parameters to temperature and the analysis of double-dip in the pressure–time profile for single crystal copper at 1250 K

Study of the size effect by accurately determining the crystal parameters

International Nuclear Information System (INIS)

Seguin, Remy

1973-01-01

The size factor η = da/adC was measured by comparing the variations in the crystal parameter as a function of the concentration, samples of Al of various degrees of purity and Al - V and Al - Cu alloys with concentrations of less than 1 000 ppm being used. The results confirm the experimental results obtained with alloys supersaturated by ultra-rapid tempering but are not consistent with theoretical values, which appear to be too large for the case of transition elements in solution in Al. The parameter was determined from Kossel diagrams obtained using an electron probe microanalyzer. The measurement methods were developed and generalized by plotting curves representing the variation of the parameter as a function of temperature between 20 and 60 deg. C. Values were obtained for the parameter at given temperatures (± 0.1 deg. C) with an accuracy of Δa/a ≅ 8.10 -6 . (author) [fr

Carboxylic acids in crystallization of macromolecules: learning from successful crystallization experiments.

Science.gov (United States)

Offermann, Lesa R; He, John Z; Mank, Nicholas J; Booth, William T; Chruszcz, Maksymilian

2014-03-01

The production of macromolecular crystals suitable for structural analysis is one of the most important and limiting steps in the structure determination process. Often, preliminary crystallization trials are performed using hundreds of empirically selected conditions. Carboxylic acids and/or their salts are one of the most popular components of these empirically derived crystallization conditions. Our findings indicate that almost 40 % of entries deposited to the Protein Data Bank (PDB) reporting crystallization conditions contain at least one carboxylic acid. In order to analyze the role of carboxylic acids in macromolecular crystallization, a large-scale analysis of the successful crystallization experiments reported to the PDB was performed. The PDB is currently the largest source of crystallization data, however it is not easily searchable. These complications are due to a combination of a free text format, which is used to capture information on the crystallization experiments, and the inconsistent naming of chemicals used in crystallization experiments. Despite these difficulties, our approach allows for the extraction of over 47,000 crystallization conditions from the PDB. Initially, the selected conditions were investigated to determine which carboxylic acids or their salts are most often present in crystallization solutions. From this group, selected sets of crystallization conditions were analyzed in detail, assessing parameters such as concentration, pH, and precipitant used. Our findings will lead to the design of new crystallization screens focused around carboxylic acids.

Order-parameter-aided temperature-accelerated sampling for the exploration of crystal polymorphism and solid-liquid phase transitions

International Nuclear Information System (INIS)

Yu, Tang-Qing; Vanden-Eijnden, Eric; Chen, Pei-Yang; Chen, Ming; Samanta, Amit; Tuckerman, Mark

2014-01-01

The problem of predicting polymorphism in atomic and molecular crystals constitutes a significant challenge both experimentally and theoretically. From the theoretical viewpoint, polymorphism prediction falls into the general class of problems characterized by an underlying rough energy landscape, and consequently, free energy based enhanced sampling approaches can be brought to bear on the problem. In this paper, we build on a scheme previously introduced by two of the authors in which the lengths and angles of the supercell are targeted for enhanced sampling via temperature accelerated adiabatic free energy dynamics [T. Q. Yu and M. E. Tuckerman, Phys. Rev. Lett. 107, 015701 (2011)]. Here, that framework is expanded to include general order parameters that distinguish different crystalline arrangements as target collective variables for enhanced sampling. The resulting free energy surface, being of quite high dimension, is nontrivial to reconstruct, and we discuss one particular strategy for performing the free energy analysis. The method is applied to the study of polymorphism in xenon crystals at high pressure and temperature using the Steinhardt order parameters without and with the supercell included in the set of collective variables. The expected fcc and bcc structures are obtained, and when the supercell parameters are included as collective variables, we also find several new structures, including fcc states with hcp stacking faults. We also apply the new method to the solid-liquid phase transition in copper at 1300 K using the same Steinhardt order parameters. Our method is able to melt and refreeze the system repeatedly, and the free energy profile can be obtained with high efficiency

CRYSTALLIZATION KINETICS OF GLASS-CERAMICS BY DIFFERENTIAL THERMAL ANALYSIS

Directory of Open Access Journals (Sweden)

A. NOZAD

2011-06-01

Full Text Available The crystallization behavior of fluorphlogopite, a glass-ceramic in the MgO–SiO2–Al2O3–K2O–B2O3–F system, was studied by substitution of Li2O for K2O in the glass composition. DTA, XRD and SEM were used for the study of crystallization behavior, formed phases and microstructure of the resulting glass-ceramics. Crystallization kinetics of the glass was investigated under non-isothermal conditions, using the formal theory of transformations for heterogeneous nucleation. The crystallization results were analyzed, and both the activation energy of crystallization process as well as the crystallization mechanism were characterized. Calculated kinetic parameters indicated that the appropriate crystallization mechanism was bulk crystallization for base glass and the sample with addition of Li2O. Non-isothermal DTA experiments showed that the crystallization activation energies of base glasses was in the range of 234-246 KJ/mol and in the samples with addition of Li2O was changed to the range of 317-322 KJ/mol.

Overexpression, purification, crystallization and preliminary X-ray crystal analysis of Bacillus pallidusd-arabinose isomerase

International Nuclear Information System (INIS)

Takeda, Kosei; Yoshida, Hiromi; Takada, Goro; Izumori, Ken; Kamitori, Shigehiro

2008-01-01

Recombinant B. pallidusd-arabinose isomerase was crystallized and diffraction data were collected to 2.3 Å resolution. d-Arabinose isomerase catalyzes the isomerization of d-arabinose to d-ribulose. Bacillus pallidusd-arabinose isomerase has broad substrate specificity and can catalyze the isomerization of d-arabinose, l-fucose, l-xylose, l-galactose and d-altrose. Recombinant B. pallidusd-arabinose isomerase was overexpressed, purified and crystallized. A crystal of the enzyme was obtained by the sitting-drop method at room temperature and belonged to the orthorhombic space group P2 1 2 1 2, with unit-cell parameters a = 144.9, b = 127.9, c = 109.5 Å. Diffraction data were collected to 2.3 Å resolution

Inverse Opal Photonic Crystals as an Optofluidic Platform for Fast Analysis of Hydrocarbon Mixtures.

Science.gov (United States)

Xu, Qiwei; Mahpeykar, Seyed Milad; Burgess, Ian B; Wang, Xihua

2018-06-13

Most of the reported optofluidic devices analyze liquid by measuring its refractive index. Recently, the wettability of liquid on various substrates has also been used as a key sensing parameter in optofluidic sensors. However, the above-mentioned techniques face challenges in the analysis of the relative concentration of components in an alkane hydrocarbon mixture, as both refractive indices and wettabilities of alkane hydrocarbons are very close. Here, we propose to apply volatility of liquid as the key sensing parameter, correlate it to the optical property of liquid inside inverse opal photonic crystals, and construct powerful optofluidic sensors for alkane hydrocarbon identification and analysis. We have demonstrated that via evaporation of hydrocarbons inside the periodic structure of inverse opal photonic crystals and observation of their reflection spectra, an inverse opal film could be used as a fast-response optofluidic sensor to accurately differentiate pure hydrocarbon liquids and relative concentrations of their binary and ternary mixtures in tens of seconds. In these 3D photonic crystals, pure chemicals with different volatilities would have different evaporation rates and can be easily identified via the total drying time. For multicomponent mixtures, the same strategy is applied to determine the relative concentration of each component simply by measuring drying time under different temperatures. Using this optofluidic sensing platform, we have determined the relative concentrations of ternary hydrocarbon mixtures with the difference of only one carbon between alkane hydrocarbons, which is a big step toward detailed hydrocarbon analysis for practical use.

Isolation, crystallization and preliminary crystallographic analysis of Salmonella typhimurium uridine phosphorylase crystallized with 2,2′-anhydrouridine

Energy Technology Data Exchange (ETDEWEB)

Timofeev, Vladimir I.; Lashkov, Alexander A.; Gabdoulkhakov, Azat G.; Pavlyuk, Bogdan Ph. [A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninskiy Prospect 59, 119333 Moscow (Russian Federation); Kachalova, Galina S. [Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Institutskaya Street 3, 142290 Pushchino, Moscow Region (Russian Federation); Betzel, Christian [Institute fur Biochemie und Lebensmittelchemie, University of Hamburg, c/o DESY, Building 22, Notkestrasse 85, 22604 Hamburg (Germany); Morgunova, Ekaterina Yu.; Zhukhlistova, Nadezhda E.; Mikhailov, Al’bert M., E-mail: amm@ns.crys.ras.ru [A. V. Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninskiy Prospect 59, 119333 Moscow (Russian Federation)

2007-10-01

S. typhimurium uridine phosphorylase has been isolated and crystallized in the presence of ligand. Uridine phosphorylase (UPh; EC 2.4.2.3) is a member of the pyrimidine nucleoside phosphorylase family of enzymes which catalyzes the phosphorolytic cleavage of the C—N glycoside bond of uridine, with the formation of ribose 1-phosphate and uracil. This enzyme has been shown to be important in the activation and catabolism of fluoropyrimidines. Modulation of its enzymatic activity may affect the therapeutic efficacy of chemotherapeutic agents. The structural investigation of the bacterial uridine phosphorylases, both unliganded and complexed with substrate/product analogues and inhibitors, may help in understanding the catalytic mechanism of the phosphorolytic cleavage of uridine. Salmonella typhimurium uridine phosphorylase has been crystallized with 2,2′-anhydrouridine. X-ray diffraction data were collected to 2.15 Å. Preliminary analysis of the diffraction data indicates that the crystal belongs to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 88.52, b = 123.98, c = 133.52 Å. The solvent content is 45.51%, assuming the presence of one hexamer molecule per asymmetric unit.

Cloning, purification, crystallization and preliminary X-ray crystallographic analysis of a cyclophilin A-like protein from Piriformospora indica

International Nuclear Information System (INIS)

Bhatt, Harshesh; Trivedi, Dipesh Kumar; Pal, Ravi Kant; Johri, Atul Kumar; Tuteja, Narendra; Bhavesh, Neel Sarovar

2012-01-01

Cyclophin A like protein from Piriformospora indica involved in salt-stress tolerance was cloned, overexpressed, purified and crystallized. The crystals obtained diffracted X-rays to 2 Å resolution and belonged to space group C222 1 . Cyclophilins are widely distributed both in eukaryotes and prokaryotes and have a primary role as peptidyl-prolyl cis–trans isomerases (PPIases). This study focuses on the cloning, expression, purification and crystallization of a salinity-stress-induced cyclophilin A (CypA) homologue from the symbiotic fungus Piriformospora indica. Crystallization experiments in the presence of 56 mM sodium phosphate monobasic monohydrate, 1.34 M potassium phosphate dibasic pH 8.2 yielded crystals that were suitable for X-ray diffraction analysis. The crystals belonged to the orthorhombic space group C222 1 , with unit-cell parameters a = 121.15, b = 144.12, c = 110.63 Å. The crystals diffracted to a resolution limit of 2.0 Å. Analysis of the diffraction data indicated the presence of three molecules of the protein per asymmetric unit (V M = 4.48 Å 3 Da −1 , 72.6% solvent content)

Crystallization and preliminary X-ray diffraction analysis of a glutathione S-transferase from Xylella fastidiosa

International Nuclear Information System (INIS)

Garcia, Wanius; Travensolo, Regiane F.; Rodrigues, Nathalia C.; Muniz, João R. C.; Caruso, Célia S.; Lemos, Eliana G. M.; Araujo, Ana Paula U.; Carrilho, Emanuel

2008-01-01

Glutathione S-transferase from X. fastidiosa (xfGST) has been overexpressed in E. coli, purified and crystallized. Diffraction data were collected to 2.23 Å. Glutathione S-transferases (GSTs) form a group of multifunctional isoenzymes that catalyze the glutathione-dependent conjugation and reduction reactions involved in the cellular detoxification of xenobiotic and endobiotic compounds. GST from Xylella fastidiosa (xfGST) was overexpressed in Escherichia coli and purified by conventional affinity chromatography. In this study, the crystallization and preliminary X-ray analysis of xfGST is described. The purified protein was crystallized by the vapour-diffusion method, producing crystals that belonged to the triclinic space group P1. The unit-cell parameters were a = 47.73, b = 87.73, c = 90.74 Å, α = 63.45, β = 80.66, γ = 94.55°. xfGST crystals diffracted to 2.23 Å resolution on a rotating-anode X-ray source

Crystallization and preliminary X-ray diffraction analysis of a glutathione S-transferase from Xylella fastidiosa

Energy Technology Data Exchange (ETDEWEB)

Garcia, Wanius, E-mail: wanius@if.sc.usp.br [Laboratório de Biofísica Molecular ‘Sérgio Mascarenhas’, Instituto de Física de São Carlos, Universidade de São Paulo (USP), São Carlos (Brazil); Travensolo, Regiane F. [Grupo de Bioanalítica, Microfabricação e Separações, Instituto de Química de São Carlos, Universidade de São Paulo (USP), São Carlos (Brazil); Rodrigues, Nathalia C.; Muniz, João R. C. [Laboratório de Biofísica Molecular ‘Sérgio Mascarenhas’, Instituto de Física de São Carlos, Universidade de São Paulo (USP), São Carlos (Brazil); Caruso, Célia S. [Grupo de Bioanalítica, Microfabricação e Separações, Instituto de Química de São Carlos, Universidade de São Paulo (USP), São Carlos (Brazil); Lemos, Eliana G. M. [Laboratório de Bioquímica de Microrganismos e de Plantas, Departamento de Tecnologia, UNESP, Jaboticabal (Brazil); Araujo, Ana Paula U. [Laboratório de Biofísica Molecular ‘Sérgio Mascarenhas’, Instituto de Física de São Carlos, Universidade de São Paulo (USP), São Carlos (Brazil); Carrilho, Emanuel, E-mail: wanius@if.sc.usp.br [Grupo de Bioanalítica, Microfabricação e Separações, Instituto de Química de São Carlos, Universidade de São Paulo (USP), São Carlos (Brazil); Laboratório de Biofísica Molecular ‘Sérgio Mascarenhas’, Instituto de Física de São Carlos, Universidade de São Paulo (USP), São Carlos (Brazil)

2008-02-01

Glutathione S-transferase from X. fastidiosa (xfGST) has been overexpressed in E. coli, purified and crystallized. Diffraction data were collected to 2.23 Å. Glutathione S-transferases (GSTs) form a group of multifunctional isoenzymes that catalyze the glutathione-dependent conjugation and reduction reactions involved in the cellular detoxification of xenobiotic and endobiotic compounds. GST from Xylella fastidiosa (xfGST) was overexpressed in Escherichia coli and purified by conventional affinity chromatography. In this study, the crystallization and preliminary X-ray analysis of xfGST is described. The purified protein was crystallized by the vapour-diffusion method, producing crystals that belonged to the triclinic space group P1. The unit-cell parameters were a = 47.73, b = 87.73, c = 90.74 Å, α = 63.45, β = 80.66, γ = 94.55°. xfGST crystals diffracted to 2.23 Å resolution on a rotating-anode X-ray source.

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

International Nuclear Information System (INIS)

Dobson, Renwick C. J.; Atkinson, Sarah C.; Gorman, Michael A.; Newman, Janet M.; Parker, Michael W.; Perugini, Matthew A.

2008-01-01

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 2 2 1 2 symmetry. The unit-cell parameters were a = b = 92.9, c = 60.4 Å. The crystal volume per protein weight (V M ) was 2.07 Å 3 Da −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

Studies on the effect of different operational parameters on the crystallization kinetics of α-lactose monohydrate single crystals in aqueous solution

Science.gov (United States)

Parimaladevi, P.; Srinivasan, K.

2014-09-01

Supersaturation dependent nucleation, size and morphology of alpha-lactose monohydrate (α-LM) crystals from aqueous solution were investigated by adopting two different crystallization methods, slow evaporation and fast evaporation, in the supersaturation range between σ=0.05 and 1.30. The induction period of nucleation is comparatively long in case of slow evaporation and is very short in case of fast evaporation process as the interconversion between α-L and β-L is uncontrollable in the former and is under control in the latter case. Moreover α-LM crystals with tomahawk morphology were obtained throughout the supersaturation range by slow evaporation method whereas crystals with tomahawk, triangular and needle-like morphologies were obtained in supersaturation ranges σ=0.05-0.5, σ=0.5-0.9 and σ=0.9-1.30 respectively by fast evaporation method. Experimentally observed nucleation parameters were verified with theoretically deuced values. It is realized that the fast evaporation method employed in the present study is found to be highly efficient in controlling the interconversion between α-L and β-L as well as in suppressing the inhibitory activity of β molecule on the nucleation and growth of α-LM crystals when compared to conventional slow evaporation method and is successful in producing the industrially preferred needle-like crystals at high supersaturation ranges.

Purification, crystallization and preliminary crystallographic analysis of a thermostable endonuclease IV from Thermotoga maritima

International Nuclear Information System (INIS)

Hughes, Ronny C.; Tomanicek, Stephen J.; Ng, Joseph D.; Coates, Leighton

2009-01-01

The overexpression, purification and crystallization of endonuclease IV from T. maritima are reported. The crystals belonged to the hexagonal space group P6 1 and diffracted to 2.36 Å resolution. The DNA-repair enzyme endonuclease IV from the thermophilic bacterium Thermotoga maritima MSB8 (reference sequence NC-000853) has been expressed in Escherichia coli and crystallized for X-ray analysis. T. maritima endonuclease IV is a 287-amino-acid protein with 32% sequence identity to E. coli endonuclease IV. The protein was purified to homogeneity and was crystallized using the sitting-drop vapor-diffusion method. The protein crystallized in space group P6 1 , with one biological molecule in the asymmetric unit, corresponding to a Matthews coefficient of 2.39 Å 3 Da −1 and 47% solvent content. The unit-cell parameters of the crystals were a = b = 123.2, c = 35.6 Å. Microseeding and further optimization yielded crystals with an X-ray diffraction limit of 2.36 Å. A single 70° data set was collected and processed, resulting in an overall R merge and a completeness of 9.5% and 99.3%, respectively

Order parameters in smectic liquid crystals[Smectics

Energy Technology Data Exchange (ETDEWEB)

Beldon, Stephen M

2001-07-01

This thesis explores some of the important mechanisms for switching in smectic liquid crystals. It is mainly concerned with the interaction of the electric field and various order parameters in smectic phases. Distortion of these order parameters and also the layer structures associated with smectics are discussed in depth. Initial work is concentrated on the electroclinic effect of commercially available FLC mixtures, where experimental results suggest the presence of non-uniformity in the molecular director profile. Two possible models are suggested assuming a variation of the order parameter {theta} through the cell. The first model assumes that the smectic layers remain bookshelf-like, and the second that the layers tilt in a vertical chevron structure when a cone angle is induced electroclinically or otherwise. The latter model is the first 'order parameter' model of an electric field induced vertical chevron. The presence of non-uniformity in the director profile is sensed by a method similar to wavelength extinction spectroscopy. Investigations are undertaken on racemic smectic materials with high dielectric biaxiality. Modelling of such a material reveals a new electroclinic effect which shows a discrete second order phase transition on application of a field. It is suggested that a bistable electroclinic effect stabilised with a high frequency ac field may be realised if a residual polarisation is present in the high biaxiality material, and that this might be useful in the displays industry. Experimental investigations of such a material confirm the above effects close to the smectic A-C transition. Finally a higher order smectic phase, the smectic I* phase, is considered. The distortion of the hexagonal bond orientational order is investigated experimentally during application of an electric field. The first dynamic model of the switching process is presented, showing good agreement with the experimental results. It is suggested that the bond

Crystallization and preliminary X-ray crystallographic analysis of recombinant β-mannosidase from Aspergillus niger

International Nuclear Information System (INIS)

Demo, Gabriel; Fliedrová, Barbora; Weignerová, Lenka; Wimmerová, Michaela

2013-01-01

β-Mannosidase from Aspergillus niger was crystallized in the presence of d-mannose and the crystal diffracted to 2.41 Å resolution. The crystal belonged to the space group P1 with unit-cell parameters a= 62.37, b = 69.73, c = 69.90 Å, α = 108.20, β = 101.51, γ = 103.20°. β-Mannosidase (EC 3.2.1.25) is an important exoglycosidase specific for the hydrolysis of terminal β-linked mannoside in various oligomeric saccharide structures. β-Mannosidase from Aspergillus niger was expressed in Pichia pastoris and purified to clear homogeneity. β-Mannosidase was crystallized in the presence of d-mannose and the crystal diffracted to 2.41 Å resolution. The crystal belonged to space group P1, with unit-cell parameters a = 62.37, b = 69.73, c = 69.90 Å, α = 108.20, β = 101.51, γ = 103.20°. The parameters derived from the data collection indicate the presence of one molecule in the asymmetric unit

A new approach to study interaction parameters in cyanobiphenyl liquid crystal binary systems

International Nuclear Information System (INIS)

Javadian, Soheila; Dalir, Nima; Gilani, Ali Ghanadzadeh; Kakemam, Jamal; Yousefi, Ali

2015-01-01

Highlights: • The phase transition of 7CB and 5CB liquid crystals studied using the DSC. • This work includes the determination of the eutectic in the 7CB/5CB mixture. • The excess functions and interaction parameters calculated in the 7CB/5CB mixtures. • The P ∗ randomicity parameter used to describe the phase transitions of C–N and N–I. • A small amount of P ∗ showed a non-random identity of the C–N phase transition. - Abstract: The phase transition of heptylcyanobiphenyl 7CB and pentylcyanobiphenyl 5CB liquid crystals was investigated using the differential scanning calorimetry DSC technique. Then, the phase transition of different compositions of 7CB/5CB binary mixture was studied to determine the eutectic point. The phase diagram of mentioned binary system in 7CB mole fraction of 0.45 at T = 273.45 K is in good agreement with that of predicted from Schroder–van Laar equation. The thermodynamic excess functions and interaction parameters were calculated to describe the phase transition physically using the non-random mixing for the first time. The P ∗ randomicity parameter was used to describe the phase transitions of C–N and N–I in which a small amount of P ∗ shows a non-random identity of C–N phase transition. Contrarily, the P ∗ is greater in N–I phase transition showing a random mixing process

Crystallization and preliminary X-ray diffraction analysis of the peptidylprolyl isomerase Par27 of Bordetella pertussis

International Nuclear Information System (INIS)

Wohlkönig, Alexandre; Hodak, Hélène; Clantin, Bernard; Sénéchal, Magalie; Bompard, Coralie; Jacob-Dubuisson, Françoise; Villeret, Vincent

2008-01-01

Par27 from B. pertussis, the prototype of a new group of parvulins has been crystallized in two different crystal forms. Proteins with both peptidylprolyl isomerase (PPIase) and chaperone activities play a crucial role in protein folding in the periplasm of Gram-negative bacteria. Few such proteins have been structurally characterized and to date only the crystal structure of SurA from Escherichia coli has been reported. Par27, the prototype of a new group of parvulins, has recently been identified. Par27 exhibits both chaperone and PPIase activities in vitro and is the first identified parvulin protein that forms dimers in solution. Par27 has been expressed in E. coli. The protein was purified using affinity and gel-filtration chromatographic techniques and crystallized in two different crystal forms. Form A, which belongs to space group P2 (unit-cell parameters a = 42.2, b = 142.8, c = 56.0 Å, β = 95.1°), diffracts to 2.8 Å resolution, while form B, which belongs to space group C222 (unit-cell parameters a = 54.6, b = 214.1, c = 57.8 Å), diffracts to 2.2 Å resolution. Preliminary diffraction data analysis agreed with the presence of one monomer in the asymmetric unit of the orthorhombic crystal form and two in the monoclinic form

Phenylacetic acid co-crystals with acridine, caffeine, isonicotinamide and nicotinamide: Crystal structures, thermal analysis, FTIR spectroscopy and Hirshfeld surface analysis

Science.gov (United States)

Amombo Noa, Francoise M.; Jacobs, Ayesha

2017-07-01

Co-crystals of phenylacetic acid (PAA) with acridine (ACR), caffeine (CAF), isonicotinamide (INM) and nicotinamide (NAM) have been successfully prepared and characterised by single crystal X-ray diffraction, FTIR spectroscopy, thermal analysis and Hirshfeld surface analysis. The ACR, INM and NAM co-crystals with PAA exhibit the carboxylic acid-pyridine heterosynthon. Furthermore the amide-amide supramolecular homosynthon is observed in the PAA co-crystals with INM and NAM as well as Nsbnd H⋯O interactions between the acid and the respective base. The CAF co-crystal exhibits hydrogen bonding between the imidazole nitrogen and the COOH group of the PAA. The compounds demonstrate different stoichiometries; for PAA·ACR and PAA·INM a 1:1 ratio is displayed, a 2:1 in 2PAA·CAF and a 2:2 in the case of 2PAA·2NAM.

Crystal optimization and preliminary diffraction data analysis of the SCAN domain of Zfp206

International Nuclear Information System (INIS)

Liang, Yu; Choo, Siew Hua; Rossbach, Michael; Baburajendran, Nithya; Palasingam, Paaventhan; Kolatkar, Prasanna R

2012-01-01

Crystals of the SCAN domain of Zfp206 are tetragonal, belonging to space group I422 with unit-cell parameters a = 67.57, c = 87.54 Å and one molecule in the asymmetric unit, and diffract to 1.85 Å resolution. Zfp206 (also named Zscan10) is a transcription factor that plays an important role in maintaining the pluripotent state of embryonic stem cells. Zfp206 is a member of the SCAN-domain family of C 2 H 2 zinc-finger transcription factors. The SCAN domain is a highly conserved motif of 84 residues which mediates the self-association of and heterodimerization between SCAN-domain family transcription factors. The SCAN domain may therefore be the key to the selective oligomerization of and may combinatorially enhance the regulatory versatility of C 2 H 2 zinc fingers. This paper describes crystallization attempts with the SCAN domain of Zfp206 (Zfp206SCAN) and optimization strategies to obtain diffraction-quality crystals. The best diffracting crystal was grown in a solution consisting of 0.3 M ammonium sulfate, 0.1 M Tris–HCl pH 8.6, 25% PEG 3350, 0.1 M ethylenediaminetetraacetic acid disodium salt dehydrate (EDTA) using the hanging-drop vapour-diffusion technique. Optimized crystals diffracted to 1.85 Å resolution and belonged to space group I422, with unit-cell parameters a = 67.57, c = 87.54 Å. A Matthews analysis indicated the presence of one Zfp206SCAN molecule per asymmetric unit

Crystallization and preliminary X-ray analysis of vicenisaminyltransferase VinC

International Nuclear Information System (INIS)

Nango, Eriko; Minami, Atsushi; Kumasaka, Takashi; Eguchi, Tadashi

2008-01-01

The crystallization of VinC, a glycosyltransferase involved in the biosynthesis of the antitumour antibiotic vicenistatin, is reported. A recombinant glycosyltransferase, VinC, from Streptomyces halstedii HC34 has been crystallized at 293 K using PEG 3350 as precipitant. The diffraction pattern of the crystal extends to 2.0 Å resolution at 100 K using synchrotron radiation at SPring-8. The crystals are orthorhombic and belong to space group I222, with unit-cell parameters a = 98.21, b = 130.39, c = 140.11 Å. The presence of two molecules per asymmetric unit gives a crystal volume per protein weight (V M ) of 2.43 Å 3 Da −1 and a solvent content of 49.5% by volume

Electronic and Structural Parameters of Phosphorus-Oxygen Bonds in Inorganic Phosphate Crystals

Science.gov (United States)

Atuchin, V. V.; Kesler, V. G.; Pervukhina, N. V.

Wide set of experimental results on binding energy of photoelectrons emitted from P 2p, P 2s, and O 1s core levels has been observed for inorganic phosphate crystals and the parameters were compared using energy differences Δ(O 1s - P 2p) and Δ (O 1s - P 2s) as most robust characteristics. Linear dependence of the binding energy difference on mean chemical bond length L(P-O) between phosphorus and oxygen atoms has been found. The functions are of the forms: Δ (O 1s - P 2p) (eV) = 375.54 + 0.146 · L(P-O) (pm) and Δ (O 1s - P 2s) (eV) = 320.77 + 0.129 · L(P-O) (pm). The dependencies are general for inorganic phosphates and may be used in quantitative component analysis of X-ray photoemission spectra of complex oxide compounds including functional groups with different coordination of P and O atoms.

Expression, crystallization and preliminary crystallographic data analysis of filamin A repeats 14–16

International Nuclear Information System (INIS)

Aguda, Adeleke Halilu; Sakwe, Amos Malle; Rask, Lars; Robinson, Robert Charles

2007-01-01

The crystallization and crystallographic data analysis of filamin repeats 14–16 are reported. Human filamin A is a 280 kDa protein involved in actin-filament cross-linking. It is structurally divided into an actin-binding headpiece (ABD) and a rod domain containing 24 immunoglobulin-like (Ig) repeats. A fragment of human filamin A (Ig repeats 14–16) was cloned and expressed in Escherichia coli and the purified protein was crystallized in 1.6 M ammonium sulfate, 2% PEG 1000 and 100 mM HEPES pH 7.5. The crystals diffracted to 1.95 Å and belong to space group P2 1 2 1 2 1 , with unit-cell parameters a = 50.63, b = 52.10, c = 98.46 Å, α = β = γ = 90°

Crystal field parameters in UCl4: Experiment versus theory

International Nuclear Information System (INIS)

Zolnierek, Z.; Gajek, Z.; Khan Malek, C.

1984-01-01

Crystal field effect on U 4+ ion with the 3 H 4 ground term in tetragonal ligand field of UCl 4 has been studied in detail. Crystal field parameters determined experimentally from optical spectroscopy and magnetic susceptibility are in good agreement with CEP sets derived from the modified point charge model and the ab initio method. Theoretical calculations lead to overestimating the A 4 4 4 > and lowering the A 2 0 2 > values in comparison to those found in the experiments. The discrepancies are, however, within an accuracy of calculations. A large reduction of expectation values of the magnetic moment operator for the eigenvectors of lowest CF levels (17.8%), determined from magnetic susceptibility, cannot be attributed to the overlap and covalency effects only. The detailed calculations have shown that the latter effects provide about 4.6% reduction of respective matrix elements, and the applied J-J mixing procedure increases this factor up to 6.5%. Since similar, as in UCl 4 , reduction factor (proportional15%) has already been observed in a number of different uranium compounds, it seems to be likely that this feature is involved in the intrinsic properties of the U 4+ ion. We endeavor to explain this effect in terms of configuration interaction mechanisms. (orig.)

Crystal field parameters in UCI 4: Experiment versus theory

Science.gov (United States)

Zolnierek, Z.; Gajek, Z.; Malek, Ch. Khan

1984-08-01

Crystal field effect on U 4+ ion with the 3H 4 ground term in tetragonal ligand field of UCl 4 has been studied in detail. Crystal field parameters determined experimentally from optical spectroscopy and magnetic susceptibility are in good agreement with CFP sets derived from the modified point charge model and the ab initio method. Theoretical calculations lead to overestimating the A44 and lowering the A02 values in comparison to those found in the experiments. The discrepancies are, however, within an accuracy of calculations. A large reduction of expectation values of the magnetic moment operator for the eigenvectors of lowest CF levels (17.8%), determined from magnetic susceptibility, cannot be attributed to the overlap and covalency effects only. The detailed calculations have shown that the latter effects provide about 4.6% reduction of respective matrix elements, and the applied J-J mixing procedure increases this factor up to 6.5%. Since similar, as in UCl 4, reduction factor(≈15%) has already been observed in a number of different uranium compounds, it seems likely that this feature is involved in the intrinsic properties of the U 4+ ion. We endeavor to explain this effect in terms of configuration interaction mechanisms.

Crystallization and preliminary X-ray analysis of Aspergillus oryzae catechol oxidase

International Nuclear Information System (INIS)

Kaljunen, Heidi; Gasparetti, Chiara; Kruus, Kristiina; Rouvinen, Juha; Hakulinen, Nina

2011-01-01

Catechol oxidase from A. oryzae was crystallized by the hanging-drop vapour-diffusion method. Catechol oxidase is an enzyme that catalyzes the oxidation of o-diphenols to the corresponding o-quinones. It is a copper-containing enzyme with a binuclear copper active site. Here, the crystallization and multiple-wavelength anomalous dispersion data collection of catechol oxidase from the mould fungus Aspergillus oryzae are described. During the purification, three forms of the enzyme (39.3, 40.5 and 44.3 kDa) were obtained. A mixture of these three forms was initially crystallized and gave crystals that diffracted to 2.5 Å resolution and belonged to space group P3 2 21, with unit-cell parameters a = b = 118.9, c = 84.5 Å, α = β = 90, γ = 120°. A preparation containing only the shorter form (39.3 kDa) produced crystals that diffracted to 2.9 Å resolution and belonged to space group P2 1 2 1 2 1 , with unit-cell parameters a = 51.8, b = 95.3, c = 139.5 Å, α = β = γ = 90°

Expression, purification, crystallization and preliminary crystallographic analysis of laminin-binding protein (Lmb) from Streptococcus agalactiae

International Nuclear Information System (INIS)

Ragunathan, Preethi; Spellerberg, Barbara; Ponnuraj, Karthe

2009-01-01

Laminin-binding protein from S. agalactiae was expressed, purified and crystallized and X-ray diffraction data were collected to 2.5 Å resolution. Laminin-binding protein (Lmb), a surface-exposed lipoprotein from Streptococcus agalactiae (group B streptococcus), mediates attachment to human laminin and plays a crucial role in the adhesion/invasion of eukaryotic host cells. However, the structural basis of laminin binding still remains unclear. In the context of detailed structural analysis, the lmb gene has been cloned, expressed in Escherichia coli, purified and crystallized. The crystals diffracted to a resolution of 2.5 Å and belonged to the monoclinic space group P2 1 , with unit-cell parameters a = 56.63, b = 70.60, c = 75.37 Å, β = 96.77°

Studies on growth, crystal structure and characterization of novel organic nicotinium trifluoroacetate single crystals

Energy Technology Data Exchange (ETDEWEB)

Dhanaraj, P.V. [Centre for Crystal Growth, SSN College of Engineering, Kalavakkam 603 110 (India); Rajesh, N.P., E-mail: rajeshnp@hotmail.com [Centre for Crystal Growth, SSN College of Engineering, Kalavakkam 603 110 (India); Sundar, J. Kalyana; Natarajan, S. [Department of Physics, Madurai Kamaraj University, Madurai 625 021 (India); Vinitha, G. [Department of Physics, Crescent Engineering College, Chennai 600 048 (India)

2011-09-15

Highlights: {yields} Good quality crystals of nicotinium trifluoroacetate in monoclinic system were grown for first time. {yields} Nicotinium trifluoroacetate crystal exhibits third order nonlinear optical properties. {yields} The optical spectrum of nicotinium trifluoroacetate crystal reveals the wide transmission in the entire range with cutoff wavelength at 286 nm. {yields} Nicotinium trifluoroacetate is a low dielectric constant material. - Abstract: An organic material, nicotinium trifluoroacetate (NTF) was synthesized and single crystals in monoclinic system were grown from aqueous solution for the first time. Its solubility and metastable zone width were estimated. The crystal structure of NTF was analyzed to reveal the molecular arrangements and the formation of hydrogen bonds in the crystal. High-resolution X-ray diffraction rocking curve measurements were performed to analyze the structural perfection of the grown crystals. Functional groups in NTF were identified by Fourier transform infrared spectral analysis. Thermal behaviour and stability of NTF were studied by thermogravimetric and differential thermal analysis and differential scanning calorimetry. Mechanical and dielectric properties of NTF crystals were analyzed. Optical studies reveal that NTF crystals are transparent in the wavelength range 286-1100 nm. The third order nonlinear optical parameters of NTF were derived by the Z-scan technique.

Cloning, purification, crystallization and preliminary X-ray analysis of the Burkholderia pseudomallei L1 ribosomal protein

International Nuclear Information System (INIS)

Abd Aziz, Abd Ghani; Ruzheinikov, Sergey N.; Sedelnikova, Svetlana E.; Mohamed, Rahmah; Nathan, Sheila; Baker, Patrick J.; Rice, David W.

2012-01-01

The L1 ribosomal protein from B. pseudomallei has been overexpressed, purified and crystallized in a form suitable for X-ray analysis. The gene encoding the L1 ribosomal protein from Burkholderia pseudomallei strain D286 has been cloned into the pETBLUE-1 vector system, overexpressed in Escherichia coli and purified. Crystals of the native protein were grown by the hanging-drop vapour-diffusion technique using PEG 3350 as a precipitant and diffracted to beyond 1.65 Å resolution. The crystals belonged to space group P2 1 2 1 2, with unit-cell parameters a = 53.6, b = 127.1, c = 31.8 Å and with a single molecule in the asymmetric unit

Purification, crystallization and preliminary crystallographic analysis of human cystathionine β-synthase

International Nuclear Information System (INIS)

Oyenarte, Iker; Majtan, Tomas; Ereño, June; Corral-Rodríguez, María Angeles; Kraus, Jan P.; Martínez-Cruz, Luis Alfonso

2012-01-01

This article describes the crystallization and preliminary crystallographic analysis of a protein construct (hCBS 516–525 ) that contains the full-length cystathionine β-synthase from Homo sapiens (hCBS) and just lacks amino-acid residues 516–525. Human cystathionine β-synthase (CBS) is a pyridoxal-5′-phosphate-dependent hemeprotein, whose catalytic activity is regulated by S-adenosylmethionine. CBS catalyzes the β-replacement reaction of homocysteine (Hcy) with serine to yield cystathionine. CBS is a key regulator of plasma levels of the thrombogenic Hcy and deficiency in CBS is the single most common cause of homocystinuria, an inherited metabolic disorder of sulfur amino acids. The properties of CBS enzymes, such as domain organization, oligomerization degree or regulatory mechanisms, are not conserved across the eukaryotes. The current body of knowledge is insufficient to understand these differences and their impact on CBS function and physiology. To overcome this deficiency, we have addressed the crystallization and preliminary crystallographic analysis of a protein construct (hCBS 516–525 ) that contains the full-length CBS from Homo sapiens (hCBS) and just lacks amino-acid residues 516–525, which are located in a disordered loop. The human enzyme yielded crystals belonging to space group I222, with unit-cell parameters a = 124.98, b = 136.33, c = 169.83 Å and diffracting X-rays to a resolution of 3.0 Å. The crystal structure appears to contain two molecules in the asymmetric unit which presumably correspond to a dimeric form of the enzyme

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

International Nuclear Information System (INIS)

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

2006-01-01

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 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 1 2 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

Analysis of Bending Waves in Phononic Crystal Beams with Defects

Directory of Open Access Journals (Sweden)

Yongqiang Guo

2018-01-01

Full Text Available Existing investigations on imperfect phononic crystal beams mainly concern periodic multi-span beams carrying either one or two channel waves with random or deterministic disorder in span-length. This paper studies the two channel bending waves in phononic crystal beams consisting of many phases of materials with defects introduced as one structural segment having different cross-sectional dimensions or material parameters. The method of reverberation-ray matrix (MRRM based on the Timoshenko beam theory, which can conduct high-frequency analysis, is extended for the theoretical analysis of dispersion and transmission of bending waves. The supercell technique and the Floquet–Bloch theorem are adopted for modeling the dispersion characteristics, and the whole finite structural model is used to calculate the transmission spectra. Experimental measurements and numerical calculations are provided to validate the displacement transmission obtained by the proposed MRRM, with the effect of damping on transmission spectra being concerned. The high-frequency calculation applicability of the proposed MRRM is also confirmed by comparing the present results with the corresponding ones either using the transfer matrix method (TMM or MRRM based on Euler—Bernoulli beam theory. The influences of defect size, defect form, and unit-cell number on the transmission spectra and the band structures are discussed. The drawn conclusions may be useful for designing or evaluating the defected phononic crystal beams in bending wave control. In addition, our conclusions are especially potential for identifying the defect location through bending wave signals.

Purification, crystallization and preliminary X-ray crystallographic analysis of chitinase from Bacillus cereus NCTU2

Energy Technology Data Exchange (ETDEWEB)

Kuo, Chueh-Yuan [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsinchu 30013,Taiwan (China); Wu, Yue-Jin [Department of Applied Chemistry, National Chiao Tung University, Hsinchu 30010,Taiwan (China); Hsieh, Yin-Cheng; Guan, Hong-Hsiang [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsinchu 30013,Taiwan (China); Tsai, Huei-Ju [Department of Applied Chemistry, National Chiao Tung University, Hsinchu 30010,Taiwan (China); Lin, Yi-Hung; Huang, Yen-Chieh; Liu, Ming-Yih [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Li, Yaw-Kuen, E-mail: ykl@cc.nctu.edu.tw [Department of Applied Chemistry, National Chiao Tung University, Hsinchu 30010,Taiwan (China); Chen, Chun-Jung, E-mail: ykl@cc.nctu.edu.tw [Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076,Taiwan (China); Department of Physics, National Tsing-Hua University, Hsinchu 30013,Taiwan (China)

2006-09-01

The crystallization of B. cereus chitinase is reported. Chitinases (EC 3.2.1.14) are found in a broad range of organisms, including bacteria, fungi and higher plants, and play different roles depending on their origin. A chitinase from Bacillus cereus NCTU2 (ChiNCTU2) capable of hydrolyzing chitin as a carbon and nitrogen nutrient has been identified as a member of the family 18 glycoside hydrolases. ChiNCTU2 of molecular weight 36 kDa has been crystallized using the hanging-drop vapour-diffusion method. According to the diffraction of chitinase crystals at 1.10 Å resolution, the crystal belongs to space group P2{sub 1}, with unit-cell parameters a = 50.79, b = 48.79, c = 66.87 Å, β = 99.31°. Preliminary analysis indicates there is one chitinase molecule in the asymmetric unit, with a solvent content of 43.4%.

Ground and excited state absorption of Ni{sup 2+} ions in MgAl{sub 2}O{sub 4}: Crystal field analysis

Energy Technology Data Exchange (ETDEWEB)

Brik, M.G. [Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103 (Japan) and Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337 (Japan)]. E-mail: brik@fukui.kyoto-u.ac.jp; Avram, N.M. [Department of Physics, West University of Timisoara, Bd. V. Parvan No. 4, 300223 Timisoara (Romania); Avram, C.N. [Department of Physics, West University of Timisoara, Bd. V. Parvan No. 4, 300223 Timisoara (Romania); Rudowicz, C. [Institute of Physics, Szczecin University of Technology, Al. Piastow 17, 70-310 Szczecin (Poland); Yeung, Y.Y. [Department of Mathematics, Science, Social Sciences and Technology, The Hong Kong Institute of Education, 10 Lo Ping Road, Tai Po, New Territories (Hong Kong); Gnutek, P. [Institute of Physics, Szczecin University of Technology, Al. Piastow 17, 70-310 Szczecin (Poland)

2007-04-25

The exchange charge model (ECM) of crystal field is utilized to provide the theoretical explanation of the ground state absorption and the excited state absorption observed for the octahedrally coordinated Ni{sup 2+} ions in the spinel MgAl{sub 2}O{sub 4}. The ECM enables modeling of the crystal field parameters (CFPs) for the impurity ions based on the crystal structure data of the host lattice. To ensure the reliability of the CFPs, the convergence of the CFP values with the increasing number of the coordination spheres taken into account in the ECM calculations is considered. The trigonal CFPs B{sub 2}{sup 0},B{sub 4}{sup 0}andB{sub 4}{sup -3} determined by the ECM, together with the appropriate Racah parameters B and C, serve as input to two crystal field analysis computer packages, which compute the energy level schemes within the whole 3d{sup 8} configuration. The cubic approximation utilizing only one CFP Dq is also discussed. Basic features of the ground and excited state absorption spectra observed for MgAl{sub 2}O{sub 4}:Ni{sup 2+} are satisfactorily explained by our crystal field analysis. In order to model the pressure dependence of the CFPs (and thus of the absorption spectra when relevant experimental data become available), the variation of the CFPs induced by possible distortions of the lattice due to, e.g. overall relaxation of the ions or accommodation of the impurity ions in the lattice, is studied. Analysis of the experimental absorption spectra enables us to evaluate also the Huang-Rhys parameter, the effective phonon energy, and the zero-phonon line position.

Multiphysical simulation analysis of the dislocation structure in germanium single crystals

Science.gov (United States)

Podkopaev, O. I.; Artemyev, V. V.; Smirnov, A. D.; Mamedov, V. M.; Sid'ko, A. P.; Kalaev, V. V.; Kravtsova, E. D.; Shimanskii, A. F.

2016-09-01

To grow high-quality germanium crystals is one of the most important problems of growth industry. The dislocation density is an important parameter of the quality of single crystals. The dislocation densities in germanium crystals 100 mm in diameter, which have various shapes of the side surface and are grown by the Czochralski technique, are experimentally measured. The crystal growth is numerically simulated using heat-transfer and hydrodynamics models and the Alexander-Haasen dislocation model in terms of the CGSim software package. A comparison of the experimental and calculated dislocation densities shows that the dislocation model can be applied to study lattice defects in germanium crystals and to improve their quality.

Crystallization and preliminary crystallographic analysis of human glycosylated haemoglobin

International Nuclear Information System (INIS)

Syakhovich, Vitaly E.; Saraswathi, N. T.; Ruff, Marc; Bokut, Sergey B.; Moras, Dino

2006-01-01

Non enzymatic modification of haemoglobin by glucose plays an important role in diabetes pathogenesis. Here the purification, characterization and crystallization of human glycosylated haemoglobin are reported. Human glycosylated haemoglobin A 1C is a stable minor variant formed in vivo by post-translational modification of the main form of haemoglobin by glucose. Crystals of oxyHbA 1C were obtained using the hanging-drop vapour-diffusion method and PEG as precipitant. The diffraction pattern of the crystal extends to a resolution of 2.3 Å at 120 K. The crystals belong to space group C2, with unit-cell parameters a = 237.98, b = 59.27, c = 137.02 Å, α = 90.00, β = 125.40, γ = 90.00°. The presence of two and a half molecules per asymmetric unit gives a crystal volume per protein weight (V M ) of 9.70 Å 3 Da −1 and a solvent content of 49%

Crystallization and preliminary crystallographic analysis of human glycosylated haemoglobin

Energy Technology Data Exchange (ETDEWEB)

Syakhovich, Vitaly E. [Department of Biochemistry and Biophysics, International Sakharov Environmental University, Dolgobrodskaya St 23, 220009 Minsk (Belarus); Saraswathi, N. T.; Ruff, Marc, E-mail: ruff@igbmc.u-strasbg.fr [Département de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch (France); Bokut, Sergey B. [Department of Biochemistry and Biophysics, International Sakharov Environmental University, Dolgobrodskaya St 23, 220009 Minsk (Belarus); Moras, Dino [Département de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch (France); Department of Biochemistry and Biophysics, International Sakharov Environmental University, Dolgobrodskaya St 23, 220009 Minsk (Belarus)

2006-02-01

Non enzymatic modification of haemoglobin by glucose plays an important role in diabetes pathogenesis. Here the purification, characterization and crystallization of human glycosylated haemoglobin are reported. Human glycosylated haemoglobin A{sub 1C} is a stable minor variant formed in vivo by post-translational modification of the main form of haemoglobin by glucose. Crystals of oxyHbA{sub 1C} were obtained using the hanging-drop vapour-diffusion method and PEG as precipitant. The diffraction pattern of the crystal extends to a resolution of 2.3 Å at 120 K. The crystals belong to space group C2, with unit-cell parameters a = 237.98, b = 59.27, c = 137.02 Å, α = 90.00, β = 125.40, γ = 90.00°. The presence of two and a half molecules per asymmetric unit gives a crystal volume per protein weight (V{sub M}) of 9.70 Å{sup 3} Da{sup −1} and a solvent content of 49%.

Cooling Crystallization of Indomethacin: Effect of Supersaturation, Temperature and Seeding on Polymorphism and Crystal Size Distribution

DEFF Research Database (Denmark)

Malwade, Chandrakant Ramkrishna; Qu, Haiyan

2018-01-01

In this work, effect of crystallization parameters i.e., supersaturation, seeding, and temperature on polymorphism and crystal size of a non-steroidal anti-inflammatory drug, indomethacin (IMC), was investigated. Firstly, several crystallization solvents (ethanol, methanol, ethyl acetate, acetone...... of IMC from ethanol confirmed that the supersaturation, operating temperature and seeding does affect the polymorphism as well as crystal size distribution of IMC. Fine needle shaped crystals of metastable α-IMC were obtained at 5 °C with high supersaturation even in presence of γ-IMC seeds, while...... rhombic plates like crystals of thermodynamically stable γ-IMC were obtained in remaining experiments. The amount of seed loading only marginally influenced the crystal growth rate and median particle diameter (d50). Particle size analysis of crystals obtained showed bimodal distribution in all...

Crystal fields at light rare-earth ions in Y and Lu

DEFF Research Database (Denmark)

Touborg, P.; Nevald, Rolf; Johansson, Torben

1978-01-01

Crystal-field parameters have been deduced for the light rare-earth solutes Ce, Pr, and Nd in Y or Lu hosts from measurements of the paramagnetic susceptibilities. In the analysis all multiplets in the lowest LS term were included. For a given host, crystal-field parameters divided by Stevens fac...

Characterization, crystallization and preliminary X-ray analysis of the adhesive domain of SdrE from Staphylococcus aureus

International Nuclear Information System (INIS)

Xiang, Hua; Gao, Fangfang; Wang, Dacheng; Liu, Jing; Hu, Jia; Zhang, Liqing; Li, Shentao; Deng, Xuming

2010-01-01

The adhesive domain of SdrE from Staphylococcus aureus was recombinantly expressed in Escherichia coli and crystallized. X-ray diffraction data were collected to 1.8 Å resolution. The adhesive domain of SdrE from Staphylococcus aureus was recombinantly expressed in Escherichia coli. The purified protein was identified by SDS–PAGE and MALDI–TOF MS. The protein was crystallized using the vapour-diffusion method in hanging-drop mode with PEG 8000 as the primary precipitating agent. X-ray diffraction data were collected to 1.8 Å resolution from a single crystal of the protein. Preliminary X-ray analysis indicated that the crystal belonged to space group P1, with unit-cell parameters a = 40.714, b = 66.355, c = 80.827 Å, α = 111.19, β = 93.99, γ = 104.39°

Crystallization and diffraction analysis of thioredoxin reductase from Streptomyces coelicolor

International Nuclear Information System (INIS)

Koháryová, Michaela; Brynda, Jiří; Řezáčová, Pavlína; Kollárová, Marta

2011-01-01

Thioredoxin reductase from S. coelicolor was crystallized and diffraction data were collected to 2.4 Å resolution. Thioredoxin reductases are homodimeric flavoenzymes that catalyze the transfer of electrons from NADPH to oxidized thioredoxin substrate. Bacterial thioredoxin reductases represent a promising target for the development of new antibiotics. Recombinant thioredoxin reductase TrxB from Streptomyces coelicolor was crystallized using the hanging-drop vapour-diffusion method. X-ray diffraction data were collected from cryocooled crystals to 2.4 Å resolution using a synchrotron-radiation source. The crystals belonged to the primitive monoclinic space group P2 1 , with unit-cell parameters a = 82.9, b = 60.6, c = 135.4 Å, α = γ = 90.0, β = 96.5°

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

International Nuclear Information System (INIS)

Rucktooa, Prakash; Huvent, Isabelle; Antoine, Rudy; Lecher, Sophie; Jacob-Dubuisson, Françoise; Villeret, Vincent; Bompard, Coralie

2006-01-01

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 1 2 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 1 2 1 2 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

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

International Nuclear Information System (INIS)

Pasquo, Alessandra; Bonamore, Alessandra; Franceschini, Stefano; Macone, Alberto; Boffi, Alberto; Ilari, Andrea

2008-01-01

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

Ab inito calculations of Hubbard parameters for NiO and Gd crystals

Directory of Open Access Journals (Sweden)

A. R Faghihi and S Jalali Asadabadi

2008-07-01

Full Text Available   In this research the Hubbard parameters have been calculated for NiO and Gd crystals, as two strongly correlated systems with partially full 3d and 4f levels, respectively. The calculations were performed within the density functional theory (DFT using the augmented plane waves plus the local orbitat (APW+lo method. We constructed a suitable supercell and found that the Hubbard parameters for the NiO and Gd compounds are equal to 5.9 eV and 5.7 eV, respectively. Our results are in good agreement with experimental data and results of other computational methods. Then we used the obtained parameters to study the structural properties of NiO and Gd by means of LDA+U approximation. Our results calculated by the LDA+U method which are in better agreement with the experiment show a significant improvement compared to the GGA approximation. The result shows that our method for calculating U parameter can be considered as a satisfactory method to study a strongly correlated system.

Certifying procedures for lead tungstate crystal parameters during mass production for the CMS ECAL

CERN Document Server

Auffray, Etiennette; Chipaux, Rémi; Drobychev, G Yu; Dromby, G; Fedorov, A A; Freire, M; Géléoc, M; Kondratev, O V; Korzhik, M V; Lecoq, P; Le Goff, J M; Letournel, P; Lopatic, A R; Missevitch, O V; Oriboni, A; Oskine, A V; Panov, B M; Peigneux, J P; Schneegans, M; Singovsky, A V; Zouevski, R F

1998-01-01

Certifying procedures and fully automated equipment for testing of Pb WO/sub 4/ (PWO) scintillators have been developed. The parameters to be verified are the optical transmission spectra in the longitudinal and transversal $9 directions; the light yield and its non-uniformity along the crystal; the scintillation kinetics; the radiation hardness and the dimensions. Both the precision of measurements and the output rate meet the stringent requirements of $9 the mass production stage of PWO scintillating elements for the CMS electromagnetic calorimeter at CERN (full characterization of several tens of crystals per day for five years). This is achieved by a) the implementation of a $9 `start- stop' technique with high count rate capability for scintillation decay measurement; b) the development of special compact fast scanning spectrophotometers; c) the application of a multi-axis movement system for crystal and $9 spectrometers; d) the use of a standard programmable 3D machine for precise dimension measurement....

Crystallization and preliminary X-ray analysis of aspartate transcarbamoylase from the parasitic protist Trypanosoma cruzi

International Nuclear Information System (INIS)

Matoba, Kazuaki; Nara, Takeshi; Aoki, Takashi; Honma, Teruki; Tanaka, Akiko; Inoue, Masayuki; Matsuoka, Shigeru; Inaoka, Daniel Ken; Kita, Kiyoshi; Harada, Shigeharu

2009-01-01

Aspartate transcarbamoylase, the second enzyme of the de novo pyrimidine-biosynthetic pathway, from T. cruzi has been purified and crystallized for X-ray structure analysis. Aspartate transcarbamoylase (ATCase), the second enzyme of the de novo pyrimidine-biosynthetic pathway, catalyzes the production of carbamoyl aspartate from carbamoyl phosphate and l-aspartate. In contrast to Escherichia coli ATCase and eukaryotic CAD multifunctional fusion enzymes, Trypanosoma cruzi ATCase lacks regulatory subunits and is not part of the multifunctional fusion enzyme. Recombinant T. cruzi ATCase expressed in E. coli was purified and crystallized in a ligand-free form and in a complex with carbamoyl phosphate at 277 K by the sitting-drop vapour-diffusion technique using polyethylene glycol 3350 as a precipitant. Ligand-free crystals (space group P1, unit-cell parameters a = 78.42, b = 79.28, c = 92.02 Å, α = 69.56, β = 82.90, γ = 63.25°) diffracted X-rays to 2.8 Å resolution, while those cocrystallized with carbamoyl phosphate (space group P2 1 , unit-cell parameters a = 88.41, b = 158.38, c = 89.00 Å, β = 119.66°) diffracted to 1.6 Å resolution. The presence of two homotrimers in the asymmetric unit (38 kDa × 6) gives V M values of 2.3 and 2.5 Å 3 Da −1 for the P1 and P2 1 crystal forms, respectively

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.

Expression, crystallization and preliminary X-ray analysis of the phosphoribosylglycinamide formyltransferase from Streptococcus mutans

International Nuclear Information System (INIS)

Zhai, Fangli; Liu, Xiaojuan; Ruan, Jing; Li, Jing; Liu, Zhenlong; Hu, Yulin; Li, Shentao

2011-01-01

Phosphoribosylglycinamide formyltransferase (PurN) from Streptococcus mutans was expressed in E. coli, purified and studied crystallographically. Phosphoribosylglycinamide formyltransferase (PurN) from Streptococcus mutans was recombinantly expressed in Escherichia coli. An effective purification protocol was established. The purified protein, which had a purity of >95%, was identified by SDS–PAGE and MALDI–TOF MS. The protein was crystallized using the vapour-diffusion method in hanging-drop mode with PEG 3350 as the primary precipitant. X-ray diffraction data were collected to 2.1 Å resolution. Preliminary X-ray analysis indicated that the crystal belonged to space group P2 1 2 1 2 1 , with unit-cell parameters a = 52.25, b = 63.29, c = 131.81 Å

Crystallization and X-ray diffraction analysis of dihydropyrimidinase from Saccharomyces kluyveri

International Nuclear Information System (INIS)

Dobritzsch, Doreen; Andersen, Birgit; Piškur, Jure

2005-01-01

Dihydropyrimidinase from the yeast S. kluyveri was crystallized by vapour diffusion. The crystals belong to space group P2 1 (unit-cell parameters a = 91.0, b = 73.0, c = 161.4 Å, β = 91.4°) and diffracted to 2.6 Å resolution. Dihydropyrimidinase (EC 3.5.2.2) catalyzes the second step in the reductive pathway of pyrimidine degradation, the hydrolysis of 5,6-dihydrouracil and 5,6-dihydrothymine to the corresponding N-carbamylated β-amino acids. Crystals of the recombinant enzyme from the yeast Saccharomyces kluyveri diffracting to 2.6 Å at a synchrotron-radiation source have been obtained by the hanging-drop vapour-diffusion method. They belong to space group P2 1 (unit-cell parameters a = 91.0, b = 73.0, c = 161.4 Å, β = 91.4°), with one homotetramer per asymmetric unit

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

International Nuclear Information System (INIS)

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

2012-01-01

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

Crystallization and preliminary X-ray diffraction analysis of phosphoglycerate kinase from Streptococcus pneumoniae

International Nuclear Information System (INIS)

Bernardo-García, Noelia; Bartual, Sergio G.; Fulde, Marcus; Bergmann, Simone; Hermoso, Juan A.

2011-01-01

Phosphoglycerate kinase, a two-domain enzyme involved in the glycolytic pathway, has been crystallized. Both the N-terminal domain and a ternary complex of the full-length enzyme with substrates were crystallized by the sitting-drop vapour-diffusion method. Inclusion of the substrates was critical in order to obtain crystals of the full-length protein. Phosphoglycerate kinase (PGK) is a widespread two-domain enzyme that plays a critical role in the glycolytic pathway. Several glycolytic enzymes from streptococci have been identified as surface-exposed proteins that are involved in streptococcal virulence by their ability to bind host proteins. This binding allows pneumococcal cells to disseminate through the epithelial and endothelial layers. Crystallization of PGK from Streptococcus pneumoniae yielded orthorhombic crystals (space group I222, unit-cell parameters a = 62.73, b = 75.38, c = 83.63 Å). However, the unit cell of these crystals was not compatible with the presence of full-length PGK. Various analytical methods showed that only the N-terminal domain of PGK was present in the I222 crystals. The ternary complex of PGK with adenylyl imidodiphosphate (AMP-PNP) and 3-phospho-d-glycerate (3PGA) produced monoclinic crystals (space group P2 1 , unit-cell parameters a = 40.35, b = 78.23, c = 59.03 Å, β = 96.34°). Molecular replacement showed that this new crystal form contained full-length PGK, thereby indicating the relevance of including substrates in order to avoid proteolysis during the crystallization process

Crystallization and preliminary X-ray analysis of dihydrodipicolinate synthase from Clostridium botulinum in the presence of its substrate pyruvate

International Nuclear Information System (INIS)

Atkinson, Sarah C.; Dobson, Renwick C. J.; Newman, Janet M.; Gorman, Michael A.; Dogovski, Con; Parker, Michael W.; Perugini, Matthew A.

2009-01-01

Dihydrodipicolinate synthase (DHDPS) catalyzes an important step in lysine biosynthesis. Here, the crystallization and preliminary diffraction analysis to 1.2 Å resolution of DHDPS from C. botulinum in the presence of its substrate pyruvate is reported. In this paper, the crystallization and preliminary X-ray diffraction analysis to near-atomic resolution of DHDPS from Clostridium botulinum crystallized in the presence of its substrate pyruvate are presented. The enzyme crystallized in a number of forms using a variety of PEG precipitants, with the best crystal diffracting to 1.2 Å resolution and belonging to space group C2, in contrast to the unbound form, which had trigonal symmetry. The unit-cell parameters were a = 143.4, b = 54.8, c = 94.3 Å, β = 126.3°. The crystal volume per protein weight (V M ) was 2.3 Å 3 Da −1 (based on the presence of two monomers in the asymmetric unit), with an estimated solvent content of 46%. The high-resolution structure of the pyruvate-bound form of C. botulinum DHDPS will provide insight into the function and stability of this essential bacterial enzyme

Strain Analysis of Stretched Tourmaline Crystals Using ImageJ, Microsoft Excel and PowerPoint

Science.gov (United States)

Bosbyshell, H.

2012-12-01

This poster describes an undergraduate structural geology lab exercise utilizing the Mohr's circle diagram for finite strain, constructed using measurements obtained from stretched tourmaline crystals. A small building housing HVAC equipment at the south end of West Chester University's Recitation Hall (itself made of serpentinite) is constructed of early-Cambrian Chickies Quartzite. Stretched tourmaline crystals, with segments joined by fibrous quartz, are visible on many surfaces (presumably originally bedding). While the original orientation of any stone is unknown, these rocks provide an opportunity for a short field exercise during a two-hour lab period and a great base for conducting strain analysis. It is always fun to ask how many in the class have ever noticed the tourmaline (few have). Students take photos using their cell phones or cameras. Since strain is a ratio the absolute size of the tourmaline crystals is immaterial. Nonetheless, this is a good opportunity to remind students of the importance of including a scale in their photographs. The photos are opened in ImageJ and the line tool is used to determine the original and final lengths of selected crystals. Students calculate strain parameters using Microsoft Excel. Then, we use Adobe Illustrator or the drafting capabilities of Microsoft PowerPoint 2010 to follow Ramsay and Huber's techniques using a Mohr's circle construction to determine the finite strain ellipse. If a stretching direction can be estimated, elongation of two crystals is all that is required to determine the strain ratio. If no stretching direction is apparent, three crystals are required for a more complicated analysis that allows for determination of the stretching direction, as well as the strain ratio.

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

International Nuclear Information System (INIS)

Lin, Yi-Hung; Peng, Wen-Yan; Huang, Yen-Chieh; Guan, Hong-Hsiang; Hsieh, Ying-Cheng; Liu, Ming-Yih; Chang, Tschining; Chen, Chun-Jung

2006-01-01

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

Overexpression, purification, crystallization and preliminary X-ray analysis of uracil N-glycosylase from Mycobacterium tuberculosis in complex with a proteinaceous inhibitor

Energy Technology Data Exchange (ETDEWEB)

Singh, Prem [Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012 (India); Talawar, Ramappa K.; Krishna, P. D. V.; Varshney, Umesh [Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012 (India); Vijayan, M., E-mail: mv@mbu.iisc.ernet.in [Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012 (India)

2006-12-01

Uracil N-glycosylase from M. tuberculosis has been crystallized in complex with a proteinaceous inhibitor (Ugi) and X-ray diffraction data have been collected. Uracil N-glycosylase is an enzyme which initiates the pathway of uracil-excision repair of DNA. The enzyme from Mycobacterium tuberculosis was co-expressed with a proteinaceous inhibitor from Bacillus subtilis phage and was crystallized in monoclinic space group C2, with unit-cell parameters a = 201.14, b = 64.27, c = 203.68 Å, β = 109.7°. X-ray data from the crystal have been collected for structure analysis.

Overexpression, purification, crystallization and preliminary X-ray analysis of uracil N-glycosylase from Mycobacterium tuberculosis in complex with a proteinaceous inhibitor

International Nuclear Information System (INIS)

Singh, Prem; Talawar, Ramappa K.; Krishna, P. D. V.; Varshney, Umesh; Vijayan, M.

2006-01-01

Uracil N-glycosylase from M. tuberculosis has been crystallized in complex with a proteinaceous inhibitor (Ugi) and X-ray diffraction data have been collected. Uracil N-glycosylase is an enzyme which initiates the pathway of uracil-excision repair of DNA. The enzyme from Mycobacterium tuberculosis was co-expressed with a proteinaceous inhibitor from Bacillus subtilis phage and was crystallized in monoclinic space group C2, with unit-cell parameters a = 201.14, b = 64.27, c = 203.68 Å, β = 109.7°. X-ray data from the crystal have been collected for structure analysis

Dielectric and electro-optical parameters of two ferroelectric liquid crystals: a comparative study

International Nuclear Information System (INIS)

Kumar Misra, Abhishek; Kumar Srivastava, Abhishek; Shukla, J P; Manohar, Rajiv

2008-01-01

Dielectric relaxation and an electro-optical study of two ferroelectric liquid crystals having different spontaneous polarizations (Felix 16/100 and Felix 17/000) showing SmC* and SmA phases have been performed in the temperature range 30-80 compfn C. The experimental data have been used to determine different relaxation parameters, viz. distribution parameter, relaxation frequency, dielectric strength and rotational viscosity. The Goldstone mode of dielectric permittivity has been well observed for both the samples under investigation. The activation energy of both the samples has also been determined by the best theoretical fitting of the Arrhenius plot. We have also evaluated the optical response time and anchoring energy coefficients from electro-optical measurement techniques for these samples.

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

International Nuclear Information System (INIS)

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

2012-01-01

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

Purification, crystallization and preliminary X-ray crystallographic analysis of diaminopimelate epimerase from Acinetobacter baumannii

International Nuclear Information System (INIS)

Park, Jeong Soon; Lee, Woo Cheol; Song, Jung Hyun; Kim, Seung Il; Lee, Je Chul; Cheong, Chaejoon; Kim, Hye-Yeon

2012-01-01

The crystallization and preliminary X-ray crystallographic analysis of diaminopimelate epimerase from A. baumannii are reported. The meso isomer of diaminopimelate (meso-DAP) is a biosynthetic precursor of l-lysine in bacteria and plants, and is a key component of the peptidoglycan layer in the cell walls of Gram-negative and some Gram-positive bacteria. Diaminopimelate epimerase (DapF) is a pyridoxal-5′-phosphate-independent racemase which catalyses the interconversion of (6S,2S)-2,6-diaminopimelic acid (ll-DAP) and meso-DAP. In this study, DapF from Acinetobacter baumannii was overexpressed in Escherichia coli strain SoluBL21, purified and crystallized using a vapour-diffusion method. A native crystal diffracted to a resolution of 1.9 Å and belonged to space group P3 1 or P3 2 , with unit-cell parameters a = b = 74.91, c = 113.35 Å, α = β = 90, γ = 120°. There were two molecules in the asymmetric unit

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

Energy Technology Data Exchange (ETDEWEB)

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

2007-09-01

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

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

International Nuclear Information System (INIS)

Saburi, Wataru; Hondoh, Hironori; Unno, Hideaki; Okuyama, Masayuki; Mori, Haruhide; Nakada, Toshitaka; Matsuura, Yoshiki; Kimura, Atsuo

2007-01-01

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

Relationship between thermodynamic parameter and thermodynamic scaling parameter for orientational relaxation time for flip-flop motion of nematic liquid crystals.

Science.gov (United States)

Satoh, Katsuhiko

2013-03-07

Thermodynamic parameter Γ and thermodynamic scaling parameter γ for low-frequency relaxation time, which characterize flip-flop motion in a nematic phase, were verified by molecular dynamics simulation with a simple potential based on the Maier-Saupe theory. The parameter Γ, which is the slope of the logarithm for temperature and volume, was evaluated under various conditions at a wide range of temperatures, pressures, and volumes. To simulate thermodynamic scaling so that experimental data at isobaric, isothermal, and isochoric conditions can be rescaled onto a master curve with the parameters for some liquid crystal (LC) compounds, the relaxation time was evaluated from the first-rank orientational correlation function in the simulations, and thermodynamic scaling was verified with the simple potential representing small clusters. A possibility of an equivalence relationship between Γ and γ determined from the relaxation time in the simulation was assessed with available data from the experiments and simulations. In addition, an argument was proposed for the discrepancy between Γ and γ for some LCs in experiments: the discrepancy arises from disagreement of the value of the order parameter P2 rather than the constancy of relaxation time τ1(*) on pressure.

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.

Understanding Crystal Populations: The Role of Textural Analysis in Determining Magmatic Timescales

Science.gov (United States)

Jerram, D. A.

2006-12-01

Crystal populations in igneous rocks that erupt at the Earths surface act as records of magma chamber processes at depth, predominantly recording episodes of growth/nucleation and geochemical changes within the host body. Detailed inspection of such crystal populations, however, reveals a complex crystal cargo that comprises crystals which have grown directly from the host, crystals that have spent one or more protracted periods being isolated from the host magma and crystals that originated from a completely different magma body and/or country rock. To further interrogate this crystal cargo we can use textural analysis techniques to fully quantify the crystal population and gather important information about the population, such as crystal morphology, spatial distribution and size relationships. When quantified, such data can be used to better constrain the different components of the resultant crystal population and how they relate to each other. Additionally, by combining textural analysis information with geochemical analysis, a powerful measure of magma timescales and magma chamber processes results. In this contribution the different types of textural analysis techniques in 2D and 3D are introduced with examples from both plutonic and volcanic systems presented to highlight the roll of this approach to quantifying magma timescales.

Thermal, mechanical, optical and dielectric properties of piperazinium hydrogen phosphite monohydrate NLO single crystal

Science.gov (United States)

Rajkumar, R.; Praveen Kumar, P.

2018-05-01

Optical transparent crystal of piperazinium hydrogen phosphite monohydrate (PHPM) was grown by slow evaporation method. The grown crystal was characterized by single crystal X-ray diffraction analysis and the crystal belongs to monoclinic system. The functional groups present in PHPM crystal were confirmed by FTIR analysis. UV-Visible spectrum shows that the PHPM crystal is transparent in the visible region. The mechanical behavior of PHPM crystal was characterized by Vickers hardness test. Thermal stability of PHPM crystal was analyzed by thermogravimetric analysis. Dielectric studies were also carried out for the grown crystal. The third-order nonlinear parameters such as nonlinear refractive index and nonlinear absorption coefficient have been calculated using Z scan technique.

Theoretical studies of spin-Hamiltonian parameters of Mo{sup 5+} ion doped in K{sub 2}SnCl{sub 6} crystal

Energy Technology Data Exchange (ETDEWEB)

Fang, Wang, E-mail: mailfangwang@163.com; Yang, Da-Xiao; Chen, Heng-Jie; Tang, Hai-Yan

2013-11-15

The spin-Hamiltonian (SH) parameters (g factors g{sub //}, g{sub ⊥} and hyperfine structure constants A{sub //}, A{sub ⊥} ) of K{sub 2}SnCl{sub 6}: Mo{sup 5+} (4d{sup 1}) crystal are theoretically studied by the use of two microscopic spin-Hamiltonian (SH) methods, the high-order perturbation theory method (PTM) and the complete diagonalization (of energy matrix) method (CDM) within the molecular orbital (MO) scheme. The contributions arising both from the crystal field and charge transfer excitations are taken into account. The investigations show that the charge transfer mechanism plays a decisive role in the understanding of the spin-Hamiltonian (SH) parameters for 4d{sup 1} ions in crystals with the strong coordinate covalence, especially for g{sub //}>g{sub ⊥} which cannot be explained in the frame work of traditional crystal field approximation (CFA). The local defect structure around Mo{sup 5+} impurity ion center is determined to be D{sub 4} {sub h} point group symmetry.

Structuring of material parameters in lithium niobate crystals with low-mass, high-energy ion radiation

Science.gov (United States)

Peithmann, K.; Eversheim, P.-D.; Goetze, J.; Haaks, M.; Hattermann, H.; Haubrich, S.; Hinterberger, F.; Jentjens, L.; Mader, W.; Raeth, N. L.; Schmid, H.; Zamani-Meymian, M.-R.; Maier, K.

2011-10-01

Ferroelectric lithium niobate crystals offer a great potential for applications in modern optics. To provide powerful optical components, tailoring of key material parameters, especially of the refractive index n and the ferroelectric domain landscape, is required. Irradiation of lithium niobate crystals with accelerated ions causes strong structured modifications in the material. The effects induced by low-mass, high-energy ions (such as 3He with 41 MeV, which are not implanted, but transmit through the entire crystal volume) are reviewed. Irradiation yields large changes of the refractive index Δn, improved domain engineering capability within the material along the ion track, and waveguiding structures. The periodic modification of Δn as well as the formation of periodically poled lithium niobate (PPLN) (supported by radiation damage) is described. Two-step knock-on displacement processes, 3He→Nb and 3He→O causing thermal spikes, are identified as origin for the material modifications.

Crystallization and preliminary crystallographic analysis of molybdenum-cofactor biosynthesis protein C from Thermus thermophilus

International Nuclear Information System (INIS)

Kanaujia, Shankar Prasad; Ranjani, Chellamuthu Vasuki; Jeyakanthan, Jeyaraman; Baba, Seiki; Chen, Lirong; Liu, Zhi-Jie; Wang, Bi-Cheng; Nishida, Masami; Ebihara, Akio; Shinkai, Akeo; Kuramitsu, Seiki; Shiro, Yoshitsugu; Sekar, Kanagaraj; Yokoyama, Shigeyuki

2006-01-01

The molybdenum-cofactor biosynthesis protein C from T. thermophilus has been crystallized in two different space groups, P2 1 and R32; the crystals diffracted to 1.9 and 1.75 Å resolution, respectively. The Gram-negative aerobic eubacterium Thermus thermophilus is an extremely important thermophilic microorganism that was originally isolated from a thermal vent environment in Japan. The molybdenum cofactor in this organism is considered to be an essential component required by enzymes that catalyze diverse key reactions in the global metabolism of carbon, nitrogen and sulfur. The molybdenum-cofactor biosynthesis protein C derived from T. thermophilus was crystallized in two different space groups. Crystals obtained using the first crystallization condition belong to the monoclinic space group P2 1 , with unit-cell parameters a = 64.81, b = 109.84, c = 115.19 Å, β = 104.9°; the crystal diffracted to a resolution of 1.9 Å. The other crystal form belonged to space group R32, with unit-cell parameters a = b = 106.57, c = 59.25 Å, and diffracted to 1.75 Å resolution. Preliminary calculations reveal that the asymmetric unit contains 12 monomers and one monomer for the crystals belonging to space group P2 1 and R32, respectively

Expression, purification, crystallization and preliminary crystallographic analysis of BipD, a component of the Burkholderia pseudomallei type III secretion system

International Nuclear Information System (INIS)

Roversi, Pietro; Johnson, Steven; Field, Terry; Deane, Janet E.; Galyov, Edouard E.; Lea, Susan M.

2006-01-01

A construct consisting of residues 10–310 of mature BipD, a component of the B. pseudomallei type III secretion system, has been crystallized. Native BipD crystals and SeMet and K 2 PtCl 4 derivative crystals have undergone preliminary crystallographic analysis. A construct consisting of residues 10–310 of BipD, a component of the Burkholderia pseudomallei type III secretion system (T3SS), has been overexpressed as a GST fusion, cleaved from the GST tag and purified. Crystals were grown of native and selenomethionine-labelled BipD. The crystals grow in two different polymorphs from the same condition. The first polymorph belongs to space group C222, with unit-cell parameters a = 103.98, b = 122.79, c = 49.17 Å, a calculated Matthews coefficient of 2.4 Å 3 Da −1 (47% solvent content) and one molecule per asymmetric unit. The second polymorph belongs to space group P2 1 2 1 2, with unit-cell parameters a = 136.47, b = 89.84, c = 50.15 Å, and a calculated Matthews coefficient of 2.3 Å 3 Da −1 (45% solvent content) for two molecules per asymmetric unit (analysis of the self-rotation function indicates the presence of a weak twofold non-crystallographic symmetry axis in this P2 1 2 1 2 form). The native crystals of both forms give diffraction data to 2.7 Å resolution, while the SeMet-labelled P2 1 2 1 2 crystals diffract to 3.3 Å resolution. A K 2 PtCl 4 derivative of the P2 1 2 1 2 form was also obtained and data were collected to 2.7 Å with radiation of wavelength λ = 0.933 Å. The Pt-derivative anomalous difference Patterson map revealed two self-peaks on the Harker sections

Microprobe channeling analysis of pyrite crystals

International Nuclear Information System (INIS)

Jamieson, D.N.; Ryan, C.G.

1992-01-01

Nuclear microprobe analysis has provided much useful information about the composition of microscopic inclusions in minerals, mainly through the use of Particle Induced X-ray Emission (PIXE). However this technique, while powerful, does not provide any direct information about the chemical state, in particular the lattice location, of the elements in the mineral. This information is often of crucial importance in understanding the ore genesis. The technique of ion channeling may be used to identify lattice location, but many minerals occur as microscopic crystals. Therefore it is necessary to utilize a nuclear microprobe with the technique of Channeling Contrast Microscopy (CCM). As many minerals contain interesting trace elements, it is necessary to measure both the yield of backscattered particles and the induced x-rays to get a clear picture of the lattice location of the elements in the crystal. CCM with PIXE was used to analyse natural pyrite crystals containing a variety of substitutional and non-substitutional elements and natural pyrite crystals from a gold bearing ore. In the latter case, evidence was obtained for two habits for Au in the 400 μm crystals: one as inclusions of Au rich minerals, the other substituted on the pyrite lattice sites. 31 refs., 3 tabs., 6 figs

Analysis of rocking curve measurements of LiF flight crystals for the objective crystal spectrometer on SPECTRUM-X-GAMMA

DEFF Research Database (Denmark)

Halm, I.; Wiebicke, H.-J.; Geppert, U.R.M.E.

1993-01-01

The Objective Crystal Spectrometer on the SPECTRUM-X-GAMMA satellite will use three types of natural crystals LiF(220), Si(111), RAP(001), and a multilayer structure providing high-resolution X- ray spectroscopy of Fe, S, O, and C line regions of bright cosmic X-ray sources. 330 - 360 LiF(220......) crystals of dimensions approximately 23 × 63 mm2 are required to cover one side of a large (1000 × 600 mm2) panel, which is to be mounted in front of one of two high throughput X- ray telescopes. Rocking curves of 441 LiF(220) crystals measured by using an expanded Cu - Kα2 beam were analyzed to select...... the main parameters of the rocking curve averaged over all crystals can be improved at least by a factor of 1.6 both in full width half maximum and peak reflectivity....

Crystal field parameters in UCl/sub 4/: Experiment versus theory

Energy Technology Data Exchange (ETDEWEB)

Zolnierek, Z.; Gajek, Z. (Polska Akademia Nauk, Wroclaw. Inst. Niskich Temperatur i Badan Strukturalnych); Khan Malek, C. (Paris-11 Univ., 91 - Orsay (France). Inst. de Physique Nucleaire)

1984-08-01

Crystal field effect on U/sup 4 +/ ion with the /sup 3/H/sub 4/ ground term in tetragonal ligand field of UCl/sub 4/ has been studied in detail. Crystal field parameters determined experimentally from optical spectroscopy and magnetic susceptibility are in good agreement with CEP sets derived from the modified point charge model and the ab initio method. Theoretical calculations lead to overestimating the A/sub 4//sup 4/ and lowering the A/sub 2//sup 0/ values in comparison to those found in the experiments. The discrepancies are, however, within an accuracy of calculations. A large similar reduction of expectation values of the magnetic moment operator for the eigenvectors of lowest CF levels (17.8%), determined from magnetic susceptibility, cannot be attributed to the overlap and covalency effects only. The detailed calculations have shown that the latter effects provide about 4.6% reduction of respective matrix elements, and the applied J-J mixing procedure increases this factor up to 6.5%. Since similar reduction factor has already been observed in a number of different uranium compounds, as in UCl/sub 4/ it seems to be likely that this feature is involved in the intrinsic properties of the U/sup 4 +/ ion. The authors endeavor to explain this effect in terms of configuration interaction mechanisms.

Crystal-field analysis of U3+ ions in K2LaX5 (X=Cl, Br or I) single crystals

Science.gov (United States)

Karbowiak, M.; Edelstein, N.; Gajek, Z.; Drożdżyński, J.

1998-11-01

An analysis of low temperature absorption spectra of U3+ ions doped in K2LaX5 (X=Cl, Br or I) single crystals is reported. The energy levels of the U3+ ion in the single crystals were assigned and fitted to a semiempirical Hamiltonian representing the combined atomic and crystal-field interactions at the Cs symmetry site. An analysis of the nephelauxetic effect and crystal-field splittings in the series of compounds is also reported.

Full 3D FDTD analysis of Electromagnetic Field in Photonic Crystal VCSEL

International Nuclear Information System (INIS)

Liu Fa; Xu Chen; Xie Yiyang; Zhao Zhenbo; Zhou Kang; Wang Baoqiang; Liu Yingming; Shen Guangdi

2011-01-01

The effect of etch damage to the mode characteristics of photonic crystal vertical cavity surface emitting lasers was simulated in this paper. The devices simulated in this paper are 850-nm GaAs-based VCSELs with photonic crystal. And the devices were simulated by using finite difference time domain (FDTD) method. Limited to the computer resource, the top DBR was simulated only, and the traverse size was smaller than the real size. In order to highlight the impact of the etch damage, several kinds of light sources and photonic crystal structures were simulated separately, and each situation is calculated in the condition of ideal photonic crystal and photonic crystal with etch damage respectively. All parameters of device and light feature are referred to the real condition.

Full 3D FDTD analysis of Electromagnetic Field in Photonic Crystal VCSEL

Energy Technology Data Exchange (ETDEWEB)

Liu Fa; Xu Chen; Xie Yiyang; Zhao Zhenbo; Zhou Kang; Wang Baoqiang; Liu Yingming; Shen Guangdi, E-mail: liufa20719@126.com [Key Laboratory of Opto-electronics Technology (Beijing University of Technology), Ministry of Education, Beijing University of Technology, 100 Ping Le Yuan, Chaoyang District, Beijing 100124 (China)

2011-02-01

The effect of etch damage to the mode characteristics of photonic crystal vertical cavity surface emitting lasers was simulated in this paper. The devices simulated in this paper are 850-nm GaAs-based VCSELs with photonic crystal. And the devices were simulated by using finite difference time domain (FDTD) method. Limited to the computer resource, the top DBR was simulated only, and the traverse size was smaller than the real size. In order to highlight the impact of the etch damage, several kinds of light sources and photonic crystal structures were simulated separately, and each situation is calculated in the condition of ideal photonic crystal and photonic crystal with etch damage respectively. All parameters of device and light feature are referred to the real condition.

Laser diffraction analysis of colloidal crystals

Energy Technology Data Exchange (ETDEWEB)

Sogami, Ikuo S.; Shinohara, Tadatomi; Yoshiyama, Tsuyoshi [Kyoto Sangyo Univ., Department of Physics, Kyoto (Japan)

2001-10-01

Laser diffraction analysis is made on crystallization in salt-free aqueous suspensions of highly-charged colloidal particles for semi-dilute specimens of concentration 0.1-10.0 vol%. Kossel diffraction patterns which represent faithfully accurate information on lattice symmetries in the suspensions enable us to investigate the time evolution of colloidal crystals. The results show that the crystallization proceeds by way of the following intermediate phase transitions: two-dimensional hcp structure {yields} random layer structure {yields} layer structure with one sliding degree of freedom {yields} stacking disorder structure {yields} stacking structure with multivariant periodicity {yields} fcc twin structure with twin plane (111) {yields} normal fcc structure {yields} bcc twin structure with twin plane (11-bar2) or (1-bar12) {yields} normal bcc structure. For concentrated suspensions (>2 vol %), the phase transition ceases to proceed at the normal fcc structure. (author)

Laser diffraction analysis of colloidal crystals

International Nuclear Information System (INIS)

Sogami, Ikuo S.; Shinohara, Tadatomi; Yoshiyama, Tsuyoshi

2001-01-01

Laser diffraction analysis is made on crystallization in salt-free aqueous suspensions of highly-charged colloidal particles for semi-dilute specimens of concentration 0.1-10.0 vol%. Kossel diffraction patterns which represent faithfully accurate information on lattice symmetries in the suspensions enable us to investigate the time evolution of colloidal crystals. The results show that the crystallization proceeds by way of the following intermediate phase transitions: two-dimensional hcp structure → random layer structure → layer structure with one sliding degree of freedom → stacking disorder structure → stacking structure with multivariant periodicity → fcc twin structure with twin plane (111) → normal fcc structure → bcc twin structure with twin plane (11-bar2) or (1-bar12) → normal bcc structure. For concentrated suspensions (>2 vol %), the phase transition ceases to proceed at the normal fcc structure. (author)

Crystallization and preliminary crystallographic analysis of recombinant immunoglobulin G-binding protein from Streptococcus suis

Energy Technology Data Exchange (ETDEWEB)

Khan, Abdul Hamid; Chu, Fuliang; Feng, Youjun; Zhang, Qinagmin [Center for Molecular Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101 (China); Qi, Jianxun [Institute of Physics, Chinese Academy of Sciences, Beijing 100080 (China); Gao, George Fu, E-mail: gaof@im.ac.cn [Center for Molecular Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101 (China)

2008-08-01

Crystallization of recombinant IgG-binding protein expressed in Escherichia coli using the hanging-drop vapour-diffusion method is described. The crystals belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 38.98, b = 43.94, c = 78.17 Å. Streptococcus suis, an important zoonotic pathogen, expresses immunoglobulin G-binding protein, which is thought to be helpful to the organism in eluding the host defence system. Recombinant IgG-binding protein expressed in Escherichia coli has been crystallized using the hanging-drop vapour-diffusion method. The crystals belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 38.98, b = 43.94, c = 78.17 Å and one molecule in the asymmetric unit. Diffraction data were collected to 2.60 Å resolution.

Crystallization and preliminary crystallographic analysis of LipC12, a true lipase isolated through a metagenomics approach

International Nuclear Information System (INIS)

Martini, V. P.; Glogauer, A.; Iulek, J.; Souza, E. M.; Pedrosa, F. O.; Krieger, N.

2012-01-01

The preliminary X-ray analysis of LipC12, the first lipase isolated through a metagenomics approach to be crystallized, is reported. LipC12, a true lipase from family I.1 of bacterial lipases which was previously isolated through a metagenomics approach, contains 293 amino acids. Among lipases of known three-dimensional structure, it has a sequence identity of 47% to the lipase from Pseudomonas aeruginosa PAO1. Recombinant N-terminally His 6 -tagged LipC12 protein was expressed in Escherichia coli, purified in a homogenous form and crystallized in several conditions, with the best crystals being obtained using 2.0 M sodium formate and 0.1 M bis-tris propane pH 7.0. X-ray diffraction data were collected to 2.70 Å resolution. The crystals belonged to the tetragonal space group P4 1 22, with unit-cell parameters a = b = 58.62, c = 192.60 Å

Effect of Metal Dopant on Ninhydrin—Organic Nonlinear Optical Single Crystals

Directory of Open Access Journals (Sweden)

R. S. Sreenivasan

2013-01-01

Full Text Available In the present work, metal (Cu2+-substituted ninhydrin single crystals were grown by slow evaporation method. The grown crystals have been subjected to single crystal XRD, powder X-ray diffraction, FTIR, dielectric and SHG studies. Single crystal X-ray diffraction analysis reveals that the compound crystallizes in monoclinic system with noncentrosymmetric space group P21 with lattice parameters a=11.28 Å, b=5.98 Å, c=5.71 Å, α=90∘, β=98.57, γ=90∘, and V=381 (Å3, which agrees very well with the reported value. The sharp and strong peaks in the powder X-ray diffraction pattern confirm the good crystallinity of the grown crystals. The presence of dopants marginally altered the lattice parameters without affecting the basic structure of the crystal. The UV-Vis transmittance spectrum shows that the crystal has a good optical transmittance in the entire visible region with lower cutoff wavelength 314 nm. The vibrational frequencies of various functional groups in the crystals have been derived from FT-IR analysis. Based on the shifts in the vibrations, the presence of copper in the lattice of the grown crystal is clearly established from the pure ninhydrin crystals. Both dielectric constant and dielectric loss decrease with the increase in frequency. The second harmonic generation efficiency was measured by employing powder Kurtz method.

Experimental parameters for quantitative surface analysis by medium energy ion scattering, ch. 1

International Nuclear Information System (INIS)

Turkenburg, W.C.; Kersten, H.H.; Colenbrander, B.G.; Jongh, A.P. de; Saris, F.W.

1976-01-01

A new UHV chamber for surface and surface layer analysis by collision spectroscopy of backscattered ions at medium energies is described. Experimental parameters like energy, angular and depth resolution, crystal alignment and background pressure are discussed. Formulae based on the use of an electrostatic energy analyser show that the analysis can be quantitative. Effects of beam induced build-up of a hydro-carbon layer, sputter cleaning and creation of radiation damage have been investigated for Cu (110) and Ni (110). Detection sensitivity for Carbon, Oxygen and Sulfur on Cu and Ni has been found to be 0.2, 0.1 and 0.03 of a monolayer respectively

Crystallization and preliminary X-ray diffraction analysis of a specific VHH domain against mouse prion protein

International Nuclear Information System (INIS)

Abskharon, Romany N. N.; Soror, Sameh H.; Pardon, Els; El Hassan, Hassan; Legname, Giuseppe; Steyaert, Jan; Wohlkonig, Alexandre

2010-01-01

The crystallization of a specific nanobody against mouse PrP C and preliminary diffraction analysis of a crystal that diffracted to 1.23 Å resolution are presented. Prion disorders are infectious diseases that are characterized by the conversion of the cellular prion protein PrP C into the pathogenic isoform PrP Sc . Specific antibodies that interact with the cellular prion protein have been shown to inhibit this transition. Recombinant VHHs (variable domain of dromedary heavy-chain antibodies) or nanobodies are single-domain antibodies, making them the smallest antigen-binding fragments. A specific nanobody (Nb-PrP-01) was raised against mouse PrP C . A crystallization condition for this recombinant nanobody was identified using high-throughput screening. The crystals were optimized using streak-seeding and the hanging-drop method. The crystals belonged to the orthorhombic space group P2 1 2 1 2 1 , with unit-cell parameters a = 30.04, b = 37.15, c = 83.00 Å, and diffracted to 1.23 Å resolution using synchrotron radiation. The crystal structure of this specific nanobody against PrP C together with the known PrP C structure may help in understanding the PrP C /PrP Sc transition mechanism

Crystallization and preliminary X-ray diffraction analysis of the lytic transglycosylase MltE from Escherichia coli

International Nuclear Information System (INIS)

Artola-Recolons, Cecilia; Llarrull, Leticia I.; Lastochkin, Elena; Mobashery, Shahriar; Hermoso, Juan A.

2010-01-01

Crystals of the lytic transglycosylase MltE from E. coli were grown using the microbatch method and diffracted to a resolution of 2.1 Å. MltE from Escherichia coli (193 amino acids, 21 380 Da) is a lytic transglycosylase that initiates the first step of cell-wall recycling. This enzyme is responsible for the cleavage of the cell-wall peptidoglycan at the β-1,4-glycosidic bond between the N-acetylglucosamine and N-acetylmuramic acid units. At the end this reaction generates a disaccharide that is internalized and initiates the recycling process. To obtain insights into the biological functions of MltE, crystallization trials were performed and crystals of MltE protein that were suitable for X-ray diffraction analysis were obtained. The MltE protein of E. coli was crystallized using the hanging-drop vapour-diffusion method at 291 K. Crystals grew from a mixture consisting of 28% polyethylene glycol 4000, 0.1 M Tris pH 8.4 and 0.2 M magnesium chloride. Further optimization was performed using the microbatch technique. Single crystals were obtained that belonged to the orthorhombic space group C222 1 , with unit-cell parameters a = 123.32, b = 183.93, c = 35.29 Å, and diffracted to a resolution of 2.1 Å

Overproduction, purification, crystallization and preliminary X-ray diffraction analysis of Trypanosoma brucei gambiense glycerol kinase

International Nuclear Information System (INIS)

Balogun, Emmanuel Oluwadare; Inaoka, Daniel Ken; Kido, Yasutoshi; Shiba, Tomoo; Nara, Takeshi; Aoki, Takashi; Honma, Teruki; Tanaka, Akiko; Inoue, Masayuki; Matsuoka, Shigeru; Michels, Paul A. M.; Harada, Shigeharu; Kita, Kiyoshi

2010-01-01

Glycerol kinase from human African trypanosomes has been purified and crystallized for X-ray structure analysis. In the bloodstream forms of human trypanosomes, glycerol kinase (GK; EC 2.7.1.30) is one of the nine glycosomally compartmentalized enzymes that are essential for energy metabolism. In this study, a recombinant Trypanosoma brucei gambiense GK (rTbgGK) with an N-terminal cleavable His 6 tag was overexpressed, purified to homogeneity and crystallized by the sitting-drop vapour-diffusion method using PEG 400 as a precipitant. A complete X-ray diffraction data set to 2.75 Å resolution indicated that the crystals belonged to the orthorhombic space group P2 1 2 1 2 1 , with unit-cell parameters a = 63.84, b = 121.50, c = 154.59 Å. The presence of two rTbgGK molecules in the asymmetric unit gives a Matthews coefficient (V M ) of 2.5 Å 3 Da −1 , corresponding to 50% solvent content

Crystallization and preliminary crystallographic analysis of l-asparaginase from Erwinia carotovora

International Nuclear Information System (INIS)

Wikman, Linnea E. K.; Krasotkina, Julya; Kuchumova, Anastasia; Sokolov, Nikolay N.; Papageorgiou, Anastassios C.

2005-01-01

Er. carotovoral-asparaginase, a potential antileukaemic agent, has been crystallized. Crystals diffract to 2.6 Å using a rotating-anode source and belong to space group P2 1 , with unit-cell parameters a = 78.0, b = 112.3, c = 78.7 Å, β = 101.9° and a homotetramer in the crystallographic asymmetric unit. Bacterial l-asparaginases have been used as therapeutic agents in the treatment of acute childhood lymphoblastic leukaemia for over 30 y. However, their use is limited owing to the glutaminase activity of the administered enzymes, which results in serious side effects. In contrast, l-asparaginase from Erwinia carotovora exhibits low glutaminase activity at physiological concentrations of l-asparagine and l-glutamine in the blood. Recombinant Er. carotovoral-asparaginase was crystallized in the presence of l-glutamate by the hanging-drop vapour-diffusion method using 10 mg ml −1 purified enzyme, 16–18%(w/v) PEG 3350 and 0.2 M NaF. X-ray diffraction data were collected to 2.6 Å at 293 K using an in-house rotating-anode generator. The crystals belong to the monoclinic P2 1 space group, with unit-cell parameters a = 78.0, b = 112.3, c = 78.7 Å, β = 101.9° and a homotetramer in the crystallographic asymmetric unit. A molecular-replacement solution has been found and refinement is currently in progress. The crystal structure may provide leads towards protein-engineering efforts aimed at safer asparaginase administration in leukaemia treatment

Novel cell parameter determination of a twisted-nematic liquid crystal display

International Nuclear Information System (INIS)

Huang Xia; Jing Hai; Fu Guozhu

2008-01-01

In this paper a novel method is proposed to determine the cell parameters including the twist angle, optic retardation and rubbing direction of twisted-nematic liquid crystal displays (TNLCD) by rotating the TNLCD. It is a single-wavelength method. Because using subtraction equation of transmittance as curve fitting equation, the influence of the light from environment and the absorption by polarizer, the sample of TNLCD and analyser on the transmittance is eliminated. Accurate results can also be obtained in imperfect darkness. By large numbers of experiments, we found that not only the experimental setup is quite simple and can be easily adopted to be carried out, but also the results are accurate

Crystallization, diffraction data collection and preliminary crystallographic analysis of DING protein from Pseudomonas fluorescens

International Nuclear Information System (INIS)

Moniot, Sebastien; Elias, Mikael; Kim, Donghyo; Scott, Ken; Chabriere, Eric

2007-01-01

Crystallization of DING protein from P. fluorescens is reported. A complete data set was collected to 1.43 Å resolution. PfluDING is a phosphate-binding protein expressed in Pseudomonas fluorescens. This protein is clearly distinct from the bacterial ABC transporter soluble phosphate-binding protein PstS and is more homologous to eukaryotic DING proteins. Interestingly, bacterial DING proteins have only been detected in certain Pseudomonas species. Although DING proteins seem to be ubiquitous in eukaryotes, they are systematically absent from eukaryotic genomic databases and thus are still quite mysterious and poorly characterized. PfluDING displays mitogenic activity towards human cells and binds various ligands such as inorganic phosphate, pyrophosphate, nucleotide triphosphates and cotinine. Here, the crystallization of PfluDING is reported in a monoclinic space group (P2 1 ), with typical unit-cell parameters a = 36.7, b = 123.7, c = 40.8 Å, α = 90, β = 116.7, γ = 90°. Preliminary crystallographic analysis reveals good diffraction quality for these crystals and a 1.43 Å resolution data set has been collected

Crystallization and preliminary X-ray analysis of βC–S lyases from two oral streptococci

International Nuclear Information System (INIS)

Kezuka, Yuichiro; Yoshida, Yasuo; Nonaka, Takamasa

2009-01-01

The βC-S lyases from two oral bacteria, Streptococcus anginosus and S. gordonii, were cloned, overproduced, purified and crystallized. The obtained crystals were characterized by X-ray diffraction. Hydrogen sulfide, which causes oral malodour, is generally produced from l-cysteine by the action of βC–S lyase from oral bacteria. The βC–S lyases from two oral bacteria, Streptococcus anginosus and S. gordonii, have been cloned, overproduced, purified and crystallized. X-ray diffraction data were collected from the two types of crystals using synchrotron radiation. The crystal of S. anginosus βC–S lyase belonged to the orthorhombic space group P2 1 2 1 2 1 , with unit-cell parameters a = 67.0, b = 111.1, c = 216.4 Å, and the crystal of S. gordonii βC–S lyase belonged to the same space group, with unit-cell parameters a = 58.0, b = 73.9. c = 187.6 Å. The structures of the βC–S lyases were solved by molecular-replacement techniques

Crystallization and preliminary X-ray crystallographic analysis of a new crystal form of hydroxylamine oxidoreductase from Nitrosomonas europaea

International Nuclear Information System (INIS)

Cedervall, Peder E.; Hooper, Alan B.; Wilmot, Carrie M.

2009-01-01

A new crystal form of N. europaea hydroxylamine oxidoreductase (space group P2 1 2 1 2) diffracted to 2.25 Å resolution at a third-generation synchrotron X-ray source. Hydroxylamine oxidoreductase (HAO) from Nitrosomonas europaea is a homotrimeric protein that catalyzes the oxidation of hydroxylamine to nitrite. Each monomer, with a molecular weight of 67.1 kDa, contains seven c-type hemes and one heme P460, the porphyrin ring of which is covalently linked to a tyrosine residue from an adjacent subunit. HAO was first crystallized and structurally characterized at a resolution of 2.8 Å in 1997. The structure was solved in space group P6 3 and suffered from merohedral twinning. Here, a crystallization procedure is presented that yielded untwinned crystals belonging to space group P2 1 2 1 2, which diffracted to 2.25 Å resolution and contained one trimer in the asymmetric unit. The unit-cell parameters were a = 140.7, b = 142.6, c = 107.4 Å

Cloning, purification, crystallization and preliminary crystallographic analysis of SecA from Enterococcus faecalis

International Nuclear Information System (INIS)

Meining, Winfried; Scheuring, Johannes; Fischer, Markus; Weinkauf, Sevil

2006-01-01

SecA ATPase from E. faecalis has been cloned, overexpressed, purified and crystallized. Crystals belong to space group C2 and diffract to 2.4 Å resolution. The gene coding for SecA from Enterococcus faecalis was cloned and overexpressed in Escherichia coli. In this protein, the lysine at position 6 was replaced by an asparagine in order to reduce sensitivity towards proteases. The modified protein was purified and crystallized. Crystals diffracting to 2.4 Å resolution were obtained using the vapour-diffusion technique. The crystals belong to the monoclinic space group C2, with unit-cell parameters a = 203.4, b = 49.8, c = 100.8 Å, α = γ = 90.0, β = 119.1°. A selenomethionine derivative was prepared and is currently being tested in crystallization trials

Crystal quality analysis and improvement using x-ray topography

International Nuclear Information System (INIS)

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

2008-01-01

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

Expression, crystallization and preliminary crystallographic analysis of RNA-binding protein Hfq (YmaH) from Bacillus subtilis in complex with an RNA aptamer.

Science.gov (United States)

Baba, Seiki; Someya, Tatsuhiko; Kawai, Gota; Nakamura, Kouji; Kumasaka, Takashi

2010-05-01

The Hfq protein is a hexameric RNA-binding protein which regulates gene expression by binding to RNA under the influence of diverse environmental stresses. Its ring structure binds various types of RNA, including mRNA and sRNA. RNA-bound structures of Hfq from Escherichia coli and Staphylococcus aureus have been revealed to have poly(A) RNA at the distal site and U-rich RNA at the proximal site, respectively. Here, crystals of a complex of the Bacillus subtilis Hfq protein with an A/G-repeat 7-mer RNA (Hfq-RNA) that were prepared using the hanging-drop vapour-diffusion technique are reported. The type 1 Hfq-RNA crystals belonged to space group I422, with unit-cell parameters a = b = 123.70, c = 119.13 A, while the type 2 Hfq-RNA crystals belonged to space group F222, with unit-cell parameters a = 91.92, b = 92.50, c = 114.92 A. Diffraction data were collected to a resolution of 2.20 A from both crystal forms. The hexameric structure of the Hfq protein was clearly shown by self-rotation analysis.

Crystal field parameters with Wannier functions: application to Nd.sub.2./sub.Fe.sub.14./sub.B systems

Czech Academy of Sciences Publication Activity Database

Yoshioka, T.; Tsuchiura, H.; Novák, Pavel

2015-01-01

Roč. 19, Sup.3 (2015), S4-S8 ISSN 1432-8917 Institutional support: RVO:68378271 Keywords : crystal field parameters * Nd-Fe-B permanent magnet Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.830, year: 2014

X-ray diffraction studies of NbTe 2 single crystal

Indian Academy of Sciences (India)

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 ...

Crystallization and preliminary crystallographic analysis of l-asparaginase from Erwinia carotovora

Energy Technology Data Exchange (ETDEWEB)

Wikman, Linnea E. K. [Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20521 (Finland); Krasotkina, Julya; Kuchumova, Anastasia; Sokolov, Nikolay N. [Institute for Biomedical Chemistry, Russian Academy of Medical Sciences, 559-B, 10 Pogodinskay St, Moscow 119121 (Russian Federation); Papageorgiou, Anastassios C., E-mail: tassos.papageorgiou@btk.fi [Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20521 (Finland)

2005-04-01

Er. carotovoral-asparaginase, a potential antileukaemic agent, has been crystallized. Crystals diffract to 2.6 Å using a rotating-anode source and belong to space group P2{sub 1}, with unit-cell parameters a = 78.0, b = 112.3, c = 78.7 Å, β = 101.9° and a homotetramer in the crystallographic asymmetric unit. Bacterial l-asparaginases have been used as therapeutic agents in the treatment of acute childhood lymphoblastic leukaemia for over 30 y. However, their use is limited owing to the glutaminase activity of the administered enzymes, which results in serious side effects. In contrast, l-asparaginase from Erwinia carotovora exhibits low glutaminase activity at physiological concentrations of l-asparagine and l-glutamine in the blood. Recombinant Er. carotovoral-asparaginase was crystallized in the presence of l-glutamate by the hanging-drop vapour-diffusion method using 10 mg ml{sup −1} purified enzyme, 16–18%(w/v) PEG 3350 and 0.2 M NaF. X-ray diffraction data were collected to 2.6 Å at 293 K using an in-house rotating-anode generator. The crystals belong to the monoclinic P2{sub 1} space group, with unit-cell parameters a = 78.0, b = 112.3, c = 78.7 Å, β = 101.9° and a homotetramer in the crystallographic asymmetric unit. A molecular-replacement solution has been found and refinement is currently in progress. The crystal structure may provide leads towards protein-engineering efforts aimed at safer asparaginase administration in leukaemia treatment.

Crystallization and preliminary X-ray analysis of AbsC, a novel regulator of antibiotic production in Streptomyces coelicolor

International Nuclear Information System (INIS)

Stevenson, Clare E. M.; Kock, Holger; Mootien, Saraspadee; Davies, Sîan C.; Bibb, Mervyn J.; Lawson, David M.

2007-01-01

A novel regulator of antibiotic production in S. coelicolor, AbsC, has been crystallized in space group P2 1 2 1 2 1 . X-ray data to 2.25 Å resolution were collected on station PX 14.1 at Daresbury. Crystals of recombinant AbsC (subunit MW = 18 313 Da; 158 amino acids), a novel regulator of antibiotic production from Streptomyces coelicolor, were grown by vapour diffusion. The protein crystallizes in space group P2 1 2 1 2 1 , with unit-cell parameters a = 43.53, b = 121.30, c = 143.75 Å. Native data to a resolution of 2.25 Å were recorded at station PX 14.1 (Daresbury) from a single crystal. Preliminary analysis of these data suggests that the asymmetric unit contains four copies of the AbsC monomer, giving an estimated solvent content of 47.0%. AbsC belongs to the MarR family of proteins that mediate ligand-responsive transcriptional control

Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the regulator AcrR from Escherichia coli

International Nuclear Information System (INIS)

Li, Ming; Qiu, Xi; Su, Chih-Chia; Long, Feng; Gu, Ruoyu; McDermott, Gerry; Yu, Edward W.

2006-01-01

The transcriptional regulator AcrR from Escherichia coli has been cloned, overexpressed, purified and crystallized and X-ray diffraction data have been collected to a resolution of 2.5 Å. This paper describes the cloning, expression, purification and preliminary X-ray data analysis of the AcrR regulatory protein. The Escherichia coli AcrR is a member of the TetR family of transcriptional regulators. It regulates the expression of the AcrAB multidrug transporter. Recombinant AcrR with a 6×His tag at the C-terminus was expressed in E. coli and purified by metal-affinity chromatography. The protein was crystallized using hanging-drop vapor diffusion. X-ray diffraction data were collected from cryocooled crystals at a synchrotron light source. The best crystal diffracted to 2.5 Å. The space group was determined to be P3 2 , with unit-cell parameters a = b = 46.61, c = 166.16 Å

Charge transport in organic crystals

Energy Technology Data Exchange (ETDEWEB)

Ortmann, Frank

2009-07-01

The understanding of charge transport is one of the central goals in the research on semiconducting crystals. For organic crystals this is particularly complicated due to the strength of the electron-phonon interaction which requires the description of a seamless transition between the limiting cases of a coherent band-transport mechanism and incoherent hopping. In this thesis, charge transport phenomena in organic crystals are studied by theoretical means. A theory for charge transport in organic crystals is developed which covers the whole temperature range from low T, where it reproduces an expression from the Boltzmann equation for band transport, via elevated T, where it generalizes Holstein's small-polaron theory to finite bandwidths, up to high T, for which a temperature dependence equal to Marcus' electron-transfer theory is obtained. Thereby, coherent band transport and thermally induced hopping are treated on equal footing while simultaneously treating the electron-phonon interaction non-perturbatively. By avoiding the approximation of narrow polaron bands the theory allows for the description of large and small polarons and serves as a starting point for computational studies. The theoretical description is completed by using ab initio material parameters for the selected crystals under study. These material parameters are taken from density functional theory calculations for durene, naphthalene, and guanine crystals. Besides the analysis of the transport mechanism, special focus is put on the study of the relationship between mobility anisotropy and structure of the crystals. This study is supported by a 3D-visualization method for the transport channels in such crystals which has been derived in this thesis. (orig.)

Crystallization and preliminary crystallographic analysis of Gibberella zeae extracellular lipase

International Nuclear Information System (INIS)

Sun, Yuna; Li, Ming; Zhang, Yan; Liu, Lifang; Liu, Ye; Liu, Zheng; Li, Xumei; Lou, Zhiyong

2008-01-01

G. zeae extracellular lipase has been overexpressed, purified and crystallized. Diffraction data were collected to 2.8 Å resolution. Fusarium head blight, one of the most destructive crop diseases, is mainly caused by Fusarium graminearum (known in its sexual stage as Gibberella zeae). F. graminearum secretes various extracellular enzymes that have been hypothesized to be involved in host infection. One of the extracellular enzymes secreted by this organism is the G. zeae extracellular lipase (GZEL), which is encoded by the FGL1 gene. In order to solve the crystal structure of GZEL and to gain a better understanding of the biological functions of the protein and of possible inhibitory mechanisms of lipase inhibitors, recombinant GZEL was crystallized at 291 K using PEG 3350 as a precipitant. A data set was collected to 2.8 Å resolution from a single flash-cooled crystal (100 K). The crystal belonged to space group P2 1 2 1 2 1 , with unit-cell parameters a = 78.4, b = 91.0, c = 195.8 Å, α = β = γ = 90°. The presence of four molecules was assumed per asymmetric unit, which gave a Matthews coefficient of 2.6 Å 3 Da −1

Crystallization and preliminary crystallographic analysis of the fourth FAS1 domain of human BigH3

International Nuclear Information System (INIS)

Yoo, Ji-Ho; Kim, EungKweon; Kim, Jongsun; Cho, Hyun-Soo

2007-01-01

The crystallization and X-ray diffraction analysis of the fourth FAS1 domain of human BigH3 are reported. The protein BigH3 is a cell-adhesion molecule induced by transforming growth factor-β (TGF-β). It consists of four homologous repeat domains known as FAS1 domains; mutations in these domains have been linked to corneal dystrophy. The fourth FAS1 domain was expressed in Escherichia coli B834 (DE3) (a methionine auxotroph) and purified by DEAE anion-exchange and gel-filtration chromatography. The FAS1 domain was crystallized using the vapour-diffusion method. A SAD diffraction data set was collected to a resolution of 2.5 Å at 100 K. The crystal belonged to space group P6 1 or P6 5 and had two molecules per asymmetric unit, with unit-cell parameters a = b = 62.93, c = 143.27 Å, α = β = 90.0, γ = 120.0°

Expression, purification, crystallization and preliminary crystallographic analysis of BipD, a component of the Burkholderia pseudomallei type III secretion system

Energy Technology Data Exchange (ETDEWEB)

Roversi, Pietro; Johnson, Steven [Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU (United Kingdom); Field, Terry [Division of Microbiology, Institute for Animal Health, Compton Laboratory, Berkshire RG20 7NN (United Kingdom); Deane, Janet E. [Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU (United Kingdom); Galyov, Edouard E. [Division of Microbiology, Institute for Animal Health, Compton Laboratory, Berkshire RG20 7NN (United Kingdom); Lea, Susan M., E-mail: susan.lea@biop.ox.ac.uk [Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU (United Kingdom); Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE (United Kingdom)

2006-09-01

A construct consisting of residues 10–310 of mature BipD, a component of the B. pseudomallei type III secretion system, has been crystallized. Native BipD crystals and SeMet and K{sub 2}PtCl{sub 4} derivative crystals have undergone preliminary crystallographic analysis. A construct consisting of residues 10–310 of BipD, a component of the Burkholderia pseudomallei type III secretion system (T3SS), has been overexpressed as a GST fusion, cleaved from the GST tag and purified. Crystals were grown of native and selenomethionine-labelled BipD. The crystals grow in two different polymorphs from the same condition. The first polymorph belongs to space group C222, with unit-cell parameters a = 103.98, b = 122.79, c = 49.17 Å, a calculated Matthews coefficient of 2.4 Å{sup 3} Da{sup −1} (47% solvent content) and one molecule per asymmetric unit. The second polymorph belongs to space group P2{sub 1}2{sub 1}2, with unit-cell parameters a = 136.47, b = 89.84, c = 50.15 Å, and a calculated Matthews coefficient of 2.3 Å{sup 3} Da{sup −1} (45% solvent content) for two molecules per asymmetric unit (analysis of the self-rotation function indicates the presence of a weak twofold non-crystallographic symmetry axis in this P2{sub 1}2{sub 1}2 form). The native crystals of both forms give diffraction data to 2.7 Å resolution, while the SeMet-labelled P2{sub 1}2{sub 1}2 crystals diffract to 3.3 Å resolution. A K{sub 2}PtCl{sub 4} derivative of the P2{sub 1}2{sub 1}2 form was also obtained and data were collected to 2.7 Å with radiation of wavelength λ = 0.933 Å. The Pt-derivative anomalous difference Patterson map revealed two self-peaks on the Harker sections.

Purification, crystallization and X-ray diffraction analysis of human dynamin-related protein 1 GTPase-GED fusion protein

International Nuclear Information System (INIS)

Klinglmayr, Eva; Wenger, Julia; Mayr, Sandra; Bossy-Wetzel, Ella; Puehringer, Sandra

2012-01-01

The crystallization and initial diffraction analysis of human Drp1 GTPase-GED fusion protein are reported. The mechano-enzyme dynamin-related protein 1 plays an important role in mitochondrial fission and is implicated in cell physiology. Dysregulation of Drp1 is associated with abnormal mitochondrial dynamics and neuronal damage. Drp1 shares structural and functional similarities with dynamin 1 with respect to domain organization, ability to self-assemble into spiral-like oligomers and GTP-cycle-dependent membrane scission. Structural studies of human dynamin-1 have greatly improved the understanding of this prototypical member of the dynamin superfamily. However, high-resolution structural information for full-length human Drp1 covering the GTPase domain, the middle domain and the GTPase effector domain (GED) is still lacking. In order to obtain mechanistic insights into the catalytic activity, a nucleotide-free GTPase-GED fusion protein of human Drp1 was expressed, purified and crystallized. Initial X-ray diffraction experiments yielded data to 2.67 Å resolution. The hexagonal-shaped crystals belonged to space group P2 1 2 1 2, with unit-cell parameters a = 53.59, b = 151.65, c = 43.53 Å, one molecule per asymmetric unit and a solvent content of 42%. Expression of selenomethionine-labelled protein is currently in progress. Here, the expression, purification, crystallization and X-ray diffraction analysis of the Drp1 GTPase-GED fusion protein are presented, which form a basis for more detailed structural and biophysical analysis

Proportion quantitative analysis and etching of {110} planes on tungsten single crystal coating surface

Energy Technology Data Exchange (ETDEWEB)

Mu, Rende, E-mail: dallasbiam@163.com [Beijing Institute of Aeronautical Materials, Aviation Key Laboratory of Science and Technology on Advanced Corrosion and Protection for Aviation Material, Department 5, P.O. Box 81-5, Beijing 100095 (China); Tan, Chengwen; Yu, Xiaodong [School of Material Science and Engineering, Beijing Institute of Technology, Beijing 100081 (China)

2016-05-05

Tungsten single crystal and poly crystal were treated by electrolytic etching in a 3% by weight solution of NaOH in distilled water. The method for determining the proportion of {110} planes and characteristic morphology on the coating surface after electrolytic etching were investigated using EBSD and auto-focusing microscope. Then the optimization of process parameters for electrolytic etching is achieved. In order to compare the effect of process parameters, three process parameters were selected for the tungsten single crystal electrolytic etching. Through analyzing the change of {110} planes' proportion, we found that when the coatings are etched with 1.4 amp/cm{sup 2} and 3 min, {110} planes can be exposed in the greatest degree that can reach 61.4% on tubular surfaces. The proposed approach greatly improves the proportion of {110} planes relative to the original surface. - Highlights: • Tungsten single/poly crystals treated by electrolytic etching in solution of NaOH. • The {110} planes have the lower surface free energy than {112}. • Some {112} planes etched firstly, the {110} planes exposed at last during etching. • {110} planes exposed to the greatest extent with 1.4 amp/cm{sup 2} and 3 min.

Purification, crystallization and preliminary X-ray analysis of the IgV domain of human nectin-4.

Science.gov (United States)

Xu, Xiang; Zhang, Xiaoai; Lu, Guangwen; Cai, Yongping

2012-08-01

Nectin-4 belongs to a family of immunoglobulin-like cell adhesion molecules and is highly expressed in cancer cells. Recently, nectin-4 was found to be a receptor of measles virus and the IgV domain sustains strong binding to measles virus H protein. In this study, the successful expression and purification of human nectin-4 V domain (nectin-4v) is reported. The purified protein was crystallized using the sitting-drop vapour-diffusion method. The crystals diffracted to 1.8 Å resolution and belonged to space group P2(1), with unit-cell parameters a = 33.1, b = 51.7, c = 56.9 Å, β = 94.7°. Preliminary analysis of the diffraction data was also performed.

Crystallization and preliminary crystallographic analysis of Axe2, an acetylxylan esterase from Geobacillus stearothermophilus

International Nuclear Information System (INIS)

Lansky, Shifra; Alalouf, Onit; Solomon, Vered; Alhassid, Anat; Govada, Lata; Chayan, Naomi E.; Belrhali, Hassan; Shoham, Yuval; Shoham, Gil

2013-01-01

The serine acetylxylan esterase from G. stearothermophilus (Axe2) has been crystallized in the tetragonal space group I422. Complete diffraction data sets have been measured for the selenomethionine derivative (SAD data, 1.70 Å resolution) and the wild-type enzyme (1.85 Å resolution) to be used for a full three-dimensional structural analysis of the Axe2 protein. Acetylxylan esterases are part of the hemi-cellulolytic system of many microorganisms which utilize plant biomass for growth. Xylans, which are polymeric sugars that constitute a significant part of the plant biomass, are usually substituted with acetyl side groups attached at position 2 or 3 of the xylose backbone units. Acetylxylan esterases hydrolyse the ester linkages of the xylan acetyl groups and thus improve the ability of main-chain hydrolysing enzymes to break down the sugar backbone units. As such, these enzymes play an important part in the hemi-cellulolytic utilization system of many microorganisms that use plant biomass for growth. Interest in the biochemical characterization and structural analysis of these enzymes stems from their numerous potential biotechnological applications. An acetylxylan esterase (Axe2) of this type from Geobacillus stearothermophilus T-6 has recently been cloned, overexpressed, purified, biochemically characterized and crystallized. One of the crystal forms obtained (RB1) belonged to the tetragonal space group I422, with unit-cell parameters a = b = 110.2, c = 213.1 Å. A full diffraction data set was collected to 1.85 Å resolution from flash-cooled crystals of the wild-type enzyme at 100 K using synchrotron radiation. A selenomethionine derivative of Axe2 has also been prepared and crystallized for single-wavelength anomalous diffraction experiments. The crystals of the selenomethionine-derivatized Axe2 appeared to be isomorphous to those of the wild-type enzyme and enabled the measurement of a full 1.85 Å resolution diffraction data set at the selenium

Crystallization and preliminary crystallographic analysis of porcine acylaminoacyl peptidase

Energy Technology Data Exchange (ETDEWEB)

Wright, Helena [Department of Biological Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL (United Kingdom); Kiss, András L.; Szeltner, Zoltán; Polgár, László [Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, H-1518 Budapest 112, PO Box 7 (Hungary); Fülöp, Vilmos, E-mail: vilmos@globin.bio.warwick.ac.uk [Department of Biological Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL (United Kingdom)

2005-10-01

Acylaminoacyl peptidase from porcine liver has been crystallized. Data were collected to 3.4 Å from native crystals and a search for heavy-atom derivatives is in progress. Acylaminoacyl peptidase (also known as acylamino-acid-releasing enzyme or acylpeptide hydrolase; EC 3.4.19.1) is an unusual member of the prolyl oligopeptidase family catalysing the hydrolysis of an N-acylated peptide to an acylamino acid and a peptide with a free N-terminus. Acylaminoacyl peptidase purified from porcine liver has been crystallized in mother liquor containing 0.1 M Tris–HCl pH 7.0, 10%(w/v) polyethylene glycol 8000, 50 mM MgCl{sub 2} and 1%(w/v) CHAPS using the hanging-drop vapour-diffusion technique. A full data set to 3.4 Å resolution was collected at ESRF beamline ID14-4 and space group C222 was assigned, with unit-cell parameters a = 84.8, b = 421.1, c = 212.0 Å and four molecules in the asymmetric unit.

Crystallization and preliminary crystallographic analysis of porcine acylaminoacyl peptidase

International Nuclear Information System (INIS)

Wright, Helena; Kiss, András L.; Szeltner, Zoltán; Polgár, László; Fülöp, Vilmos

2005-01-01

Acylaminoacyl peptidase from porcine liver has been crystallized. Data were collected to 3.4 Å from native crystals and a search for heavy-atom derivatives is in progress. Acylaminoacyl peptidase (also known as acylamino-acid-releasing enzyme or acylpeptide hydrolase; EC 3.4.19.1) is an unusual member of the prolyl oligopeptidase family catalysing the hydrolysis of an N-acylated peptide to an acylamino acid and a peptide with a free N-terminus. Acylaminoacyl peptidase purified from porcine liver has been crystallized in mother liquor containing 0.1 M Tris–HCl pH 7.0, 10%(w/v) polyethylene glycol 8000, 50 mM MgCl 2 and 1%(w/v) CHAPS using the hanging-drop vapour-diffusion technique. A full data set to 3.4 Å resolution was collected at ESRF beamline ID14-4 and space group C222 was assigned, with unit-cell parameters a = 84.8, b = 421.1, c = 212.0 Å and four molecules in the asymmetric unit

Synthesis, Crystal Structure, and Topology-Symmetry Analysis of a New Modification of NaIn[IO3]4

Science.gov (United States)

Belokoneva, E. L.; Karamysheva, A. S.; Dimitrova, O. V.; Volkov, A. S.

2018-01-01

Crystals of new iodate NaIn[IO3]4 were prepared by the hydrothermal synthesis. The unit cell parameters are a = 7.2672(2) Å, b = 15.2572(6) Å, c = 15.0208(6) Å, β = 101.517(3)°, sp. gr. P21/ c. The formula was determined during the structure determination and refinement of a twinned crystal based on a set of reflections from the atomic planes of the major individual. The refinement with anisotropic displacement parameters was performed for both twin components to the final R factor of 0.050. The In and Na atoms are in octahedral coordination formed by oxygen atoms. The oxygen octahedra are arranged into columns by sharing edges, and the columns are connected by isolated umbrella-like [IO3]- groups to form layers. The new structure is most similar to the isoformular iodate NaIn[IO3]4, which crystallizes in the same sp. gr. P21/ c and is structurally similar, but has a twice smaller unit cell and is characterized by another direction of the monoclinic axis. The structural similarity and difference between the two phases were studied by topologysymmetry analysis. The formation of these phases is related to different combinations of identical one-dimensional infinite chains of octahedra.

Development of high-performance X-ray transparent crystallization plates for in situ protein crystal screening and analysis

Energy Technology Data Exchange (ETDEWEB)

Soliman, Ahmed S. M.; Warkentin, Matthew [Cornell University, Ithaca, New York (United States); Apker, Benjamin [MiTeGen LLC, Ithaca, New York (United States); Thorne, Robert E., E-mail: ret6@cornell.edu [Cornell University, Ithaca, New York (United States); MiTeGen LLC, Ithaca, New York (United States)

2011-07-01

An optically, UV and X-ray transparent crystallization plate suitable for in situ analysis has been developed. The plate uses contact line pinning rather than wells to confine the liquids. X-ray transparent crystallization plates based upon a novel drop-pinning technology provide a flexible, simple and inexpensive approach to protein crystallization and screening. The plates consist of open cells sealed top and bottom by thin optically, UV and X-ray transparent films. The plates do not need wells or depressions to contain liquids. Instead, protein drops and reservoir solution are held in place by rings with micrometre dimensions that are patterned onto the bottom film. These rings strongly pin the liquid contact lines, thereby improving drop shape and position uniformity, and thus crystallization reproducibility, and simplifying automated image analysis of drop contents. The same rings effectively pin solutions containing salts, proteins, cryoprotectants, oils, alcohols and detergents. Strong pinning by rings allows the plates to be rotated without liquid mixing to 90° for X-ray data collection or to be inverted for hanging-drop crystallization. The plates have the standard SBS format and are compatible with standard liquid-handling robots.

Expression, purification, crystallization and preliminary X-ray analysis of maleylacetate reductase from Burkholderia sp. strain SJ98

International Nuclear Information System (INIS)

Chauhan, Archana; Islam, Zeyaul; Jain, Rakesh Kumar; Karthikeyan, Subramanian

2009-01-01

Purification and preliminary X-ray crystallographic analysis of maleylacetate reductase encoded by the pnpD gene is reported. Maleylacetate reductase (EC 1.3.1.32) is an important enzyme that is involved in the degradation pathway of aromatic compounds and catalyzes the reduction of maleylacetate to 3-oxoadipate. The gene pnpD encoding maleylacetate reductase in Burkholderia sp. strain SJ98 was cloned, expressed in Escherichia coli and purified by affinity chromatography. The enzyme was crystallized in both native and SeMet-derivative forms by the sitting-drop vapour-diffusion method using PEG 3350 as a precipitant at 293 K. The crystals belonged to space group P2 1 2 1 2, with unit-cell parameters a = 72.91, b = 85.94, c = 53.07 Å. X-ray diffraction data for the native and SeMet-derivative crystal were collected to 2.7 and 2.9 Å resolution, respectively

Link between optical spectra, crystal-field parameters, and local environments of Eu3+ ions in Eu2O3-doped sodium disilicate glass

International Nuclear Information System (INIS)

Qin, T.; Mountjoy, G.; Afify, N. D.; Reid, M. F.; Yeung, Y. Y.; Speghini, A.; Bettinelli, M.

2011-01-01

Rare-earth-doped glasses are key materials for optical technology due to the luminescent properties of 4f n ions. The crystal-field model describes the effect of local environment on transitions between 4f electrons. We present a detailed modeling study of the optical spectra of sodium disilicate glass, 33Na 2 O·67SiO 2 , doped with 0.2% and 1.0 mol%Eu 2 O 3 . This study uses very large molecular dynamics models with up to 100 Eu 3+ ions, the superposition model for covalent and overlap effects on crystal-field parameters, and realistic values for homogeneous linewidth broadening. The simulated spectra are in reasonable agreement with experiment. The trends in 7 F J energy levels across different Eu 3+ ion sites have been examined and a very detailed analysis is presented that looks at how features of the spectra are related to features of the local environment of Eu 3+ ions. Increasing the crystal-field strength S total causes the 7 F 0 energy level to decrease and causes the splitting of 7 F J manifolds to increase, and this is due to increasing mixing of 4f wave functions. To a reasonable approximation the crystal-field strength components S k depend on angular positions of ligands independently of distances to ligands. The former are seen to be more significant in determining S k , which are closely related to the rotationally invariant bond-orientational order parameters Q k . The values of S 2 are approximately linear in Q 2 , and the values of Q 2 are higher for fivefold than sixfold coordinated rare-earth ions. These results can be of importance for efforts to enhance the local environment of rare-earth ions in oxide glasses for optical applications.

A study on the microstructural parameters of 550 keV electron irradiated Lexan polymer films

International Nuclear Information System (INIS)

Hareesh, K.; Pramod, R.; Petwal, V. C.; Dwivedi, Jishnu; Sangappa; Sanjeev, Ganesh

2012-01-01

Lexan polymer films irradiated with 550 keV Electron Beam (EB) were characterized using Wide Angle Xray Scattering (WAXS) data to study the microstructural parameters. The crystal imperfection parameters like crystal size , lattice strain (g in %) and enthalpy (α) have been determined by Line Profile Analysis (LPA) using Fourier method of Warren.

Crystal-Chemical Analysis Martian Minerals in Gale Crater

Science.gov (United States)

Morrison, S. M.; Downs, R. T.; Blake, D. F.; Bish, D. L.; Ming, D. W.; Morris, R. V.; Yen, A. S.; Chipera, S. J.; Treiman, A. H.; Vaniman, D. T.;

Expression, crystallization and preliminary crystallographic analysis of RNA-binding protein Hfq (YmaH) from Bacillus subtilis in complex with an RNA aptamer

International Nuclear Information System (INIS)

Baba, Seiki; Someya, Tatsuhiko; Kawai, Gota; Nakamura, Kouji; Kumasaka, Takashi

2010-01-01

The RNA-binding protein Hfq from B. subtilis was crystallized using the hanging-drop vapour-diffusion method in two crystal forms that belonged to space groups I422 and F222; diffraction data were collected to 2.2 Å resolution from both forms. The Hfq protein is a hexameric RNA-binding protein which regulates gene expression by binding to RNA under the influence of diverse environmental stresses. Its ring structure binds various types of RNA, including mRNA and sRNA. RNA-bound structures of Hfq from Escherichia coli and Staphylococcus aureus have been revealed to have poly(A) RNA at the distal site and U-rich RNA at the proximal site, respectively. Here, crystals of a complex of the Bacillus subtilis Hfq protein with an A/G-repeat 7-mer RNA (Hfq–RNA) that were prepared using the hanging-drop vapour-diffusion technique are reported. The type 1 Hfq–RNA crystals belonged to space group I422, with unit-cell parameters a = b = 123.70, c = 119.13 Å, while the type 2 Hfq–RNA crystals belonged to space group F222, with unit-cell parameters a = 91.92, b = 92.50, c = 114.92 Å. Diffraction data were collected to a resolution of 2.20 Å from both crystal forms. The hexameric structure of the Hfq protein was clearly shown by self-rotation analysis

Recombinant production, crystallization and preliminary X-ray analysis of PCNA from the psychrophilic archaeon Methanococcoides burtonii DSM 6242

International Nuclear Information System (INIS)

Byrne-Steele, Miranda L.; Hughes, Ronny C.; Ng, Joseph D.

2009-01-01

The proliferating cell nuclear antigen (PCNA) from the eurypsychrophilic archaeon M. burtonii DSM 6242 has been cloned, overproduced, purified and crystallized. Crystals were deemed to be suitable for X-ray analysis and structure determination to 2.40 Å resolution. Proliferating cell nuclear antigen (PCNA) is a DNA-clamping protein that is responsible for increasing the processivity of the replicative polymerases during DNA replication and repair. The PCNA from the eurypsychrophilic archaeon Methanococcoides burtonii DSM 6242 (MbPCNA) has been targeted for protein structural studies. A recombinant expression system has been created that overproduces MbPCNA with an N-terminal hexahistidine affinity tag in Escherichia coli. As a result, recombinant MbPCNA with a molecular mass of 28.3 kDa has been purified to at least 95% homogeneity and crystallized by vapor-diffusion equilibration. Preliminary X-ray analysis revealed a trigonal hexagonal R3 space group, with unit-cell parameters a = b = 102.5, c = 97.5 Å. A single MbPCNA crystal was subjected to complete diffraction data-set collection using synchrotron radiation and reflections were measured to 2.40 Å resolution. The diffraction data were of suitable quality for indexing and scaling and an unrefined molecular-replacement solution has been obtained

Crystallization and preliminary X-ray crystallographic analysis of peptide deformylase from Pseudomonas aeruginosa.

Science.gov (United States)

Kim, Hyung-Wook; Han, Byung Woo; Yoon, Hye-Jin; Yang, Jin Kuk; Lee, Byung Il; Lee, Hyung Ho; Ahn, Hyung Jun; Suh, Se Won

2002-10-01

Peptide deformylase (PDF) from the pathogenic bacterium Pseudomonas aeruginosa has been overexpressed in Escherichia coli and crystallized in the presence of its inhibitor actinonin at 297 K using polyethylene glycol (PEG) 4000 as a precipitant. The diffraction limit and the spot shape of the crystals could be slightly improved by the crystal annealing/dehydration procedure. X-ray diffraction data to 1.85 A have been collected using synchrotron radiation. The crystal belongs to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 68.75, b = 74.46, c = 77.18 A. The asymmetric unit contains two subunits of peptide deformylase, with a corresponding crystal volume per protein mass (V(M)) of 2.45 A(3) Da(-1) and a solvent content of 49.8%.

Crystallization and preliminary crystallographic analysis of selenomethionine-labelled progesterone 5β-reductase from Digitalis lanata Ehrh

Energy Technology Data Exchange (ETDEWEB)

Egerer-Sieber, Claudia [Lehrstuhl für Biotechnik, Institut für Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestrasse 91, D-91052 Erlangen (Germany); Herl, Vanessa; Müller-Uri, Frieder; Kreis, Wolfgang [Lehrstuhl für Pharmazeutische Biologie, Institut für Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstrasse 5, D-91058 Erlangen (Germany); Muller, Yves A., E-mail: ymuller@biologie.uni-erlangen.de [Lehrstuhl für Biotechnik, Institut für Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestrasse 91, D-91052 Erlangen (Germany)

2006-03-01

Progesterone 5β-reductase is the first stereospecific enzyme in the pathway for the synthesis of cardenolides. To elucidate the structural mechanism of this reaction, we crystallized the selenomethionine-labelled enzyme from D. lanata and report the preliminary analysis of a MAD data set collected from these crystals. Progesterone 5β-reductase (5β-POR) catalyzes the reduction of progesterone to 5β-pregnane-3,20-dione and is the first stereospecific enzyme in the putative biosynthetic pathway of Digitalis cardenolides. Selenomethionine-derivatized 5β-POR from D. lanata was successfully overproduced and crystallized. The crystals belong to space group P4{sub 3}2{sub 1}2, with unit-cell parameters a = 71.73, c = 186.64 Å. A MAD data set collected at 2.7 Å resolution allowed the identification of six out of eight possible Se-atom positions. A first inspection of the MAD-phased electron-density map shows that 5β-POR is a Rossmann-type reductase and the quality of the map is such that it is anticipated that a complete atomic model of 5β-POR will readily be built.

Cloning, expression, purification, crystallization and preliminary X-ray analysis of the human RuvBL1–RuvBL2 complex

International Nuclear Information System (INIS)

Gorynia, Sabine; Matias, Pedro M.; Bandeiras, Tiago M.; Donner, Peter; Carrondo, Maria Arménia

2008-01-01

A truncated variant of the human RuvBL1–RuvBL2 complex was cloned, expressed, purified and crystallised. Synchrotron diffraction data to 4 Å resolution were used to carry out a preliminary crystallographic analysis of the complex. The complex of RuvBL1 and its homologue RuvBL2, two evolutionarily highly conserved eukaryotic proteins belonging to the AAA + (ATPase associated with diverse cellular activities) family of ATPases, was co-expressed in Escherichia coli. For crystallization purposes, the flexible domains II of RuvBL1 and RuvBL2 were truncated. The truncated RuvBL1–RuvBL2 complex was crystallized using the hanging-drop vapour-diffusion method at 293 K. The crystals were hexagonal-shaped plates and belonged to either the orthorhombic space group C222 1 , with unit-cell parameters a = 111.4, b = 188.0, c = 243.4 Å and six monomers in the asymmetric unit, or the monoclinic space group P2 1 , with unit-cell parameters a = 109.2, b = 243.4, c = 109.3 Å, β = 118.7° and 12 monomers in the asymmetric unit. The crystal structure could be solved by molecular replacement in both possible space groups and the solutions obtained showed that the complex forms a dodecamer

Crystallization study of Sn additive Se–Te chalcogenide alloys

Energy Technology Data Exchange (ETDEWEB)

Abdel-Rahim, M.A.; Gaber, A.; Abu-Sehly, A.A.; Abdelazim, N.M., E-mail: nana841@hotmail.co.uk

2013-08-20

Highlights: • The aim of the work deals with studying the crystallization kinetics by using different method. • Values of various kinetic parameters were calculated. • The results indicate that the rate of crystallization is related to the thermal stability and glass forming ability. - Abstract: Results of differential thermal analysis (DTA) under non-isothermal conditions of glasses Se{sub 90−x}Te{sub 10}Sn{sub x} (x = 0, 2.5, 5 and 7 at.%) are reported and discussed. The glass transition temperature (T{sub g}), the onset crystallization temperature (T{sub c}) and the peak temperature of crystallization (T{sub p}) were found to be dependent on the compositions and the heating rate. Values of various kinetic parameters such as activation energy of glass transition (E{sub g}), activation energy of crystallization (E{sub c}), rate constant (K{sub p}), Hurby number (H{sub r}) and the order parameter (n) were determined. For the present systems, the results indicate that the rate of crystallization is related to thermal stability and glass forming ability (GFA). According to the Avrami exponent (n), the results show a one dimensional growth for the composition Se{sub 90}Te{sub 10} and a three dimensional growth for the three other compositions. The crystalline phases resulting from DTA and (SEM) have been identified using X-ray diffraction.

AACSD: An atomistic analyzer for crystal structure and defects

Science.gov (United States)

Liu, Z. R.; Zhang, R. F.

2018-01-01

We have developed an efficient command-line program named AACSD (Atomistic Analyzer for Crystal Structure and Defects) for the post-analysis of atomic configurations generated by various atomistic simulation codes. The program has implemented not only the traditional filter methods like the excess potential energy (EPE), the centrosymmetry parameter (CSP), the common neighbor analysis (CNA), the common neighborhood parameter (CNP), the bond angle analysis (BAA), and the neighbor distance analysis (NDA), but also the newly developed ones including the modified centrosymmetry parameter (m-CSP), the orientation imaging map (OIM) and the local crystallographic orientation (LCO). The newly proposed OIM and LCO methods have been extended for all three crystal structures including face centered cubic, body centered cubic and hexagonal close packed. More specially, AACSD can be easily used for the atomistic analysis of metallic nanocomposite with each phase to be analyzed independently, which provides a unique pathway to capture their dynamic evolution of various defects on the fly. In this paper, we provide not only a throughout overview on various theoretical methods and their implementation into AACSD program, but some critical evaluations, specific testing and applications, demonstrating the capability of the program on each functionality.

Crystallization and preliminary crystallographic analysis of hygromycin B phosphotransferase from Escherichia coli

International Nuclear Information System (INIS)

Iino, Daisuke; Takakura, Yasuaki; Kuroiwa, Mika; Kawakami, Ryouta; Sasaki, Yasuyuki; Hoshino, Takayuki; Ohsawa, Kanju; Nakamura, Akira; Yajima, Shunsuke

2007-01-01

The crystallization and preliminary X-ray studies of the aminoglycoside antibiotic-modifying enzyme hygromycin B phosphotransferase from E. coli are reported. Aminoglycoside antibiotics, such as hygromycin, kanamycin, neomycin, spectinomycin and streptomycin, inhibit protein synthesis by acting on bacterial and eukaryotic ribosomes. Hygromycin B phosphotransferase (Hph; EC 2.7.1.119) converts hygromycin B to 7′′-O-phosphohygromycin using a phosphate moiety from ATP, resulting in the loss of its cell-killing activity. The Hph protein has been crystallized for the first time using a thermostable mutant and the hanging-drop vapour-diffusion method. The crystal provided diffraction data to a resolution of 2.1 Å and belongs to space group P3 2 21, with unit-cell parameters a = b = 71.0, c = 125.0 Å. Crystals of complexes of Hph with hygromycin B and AMP-PNP or ADP have also been obtained in the same crystal form as that of the apoprotein

Expression, crystallization and preliminary X-ray data analysis of NT-Als9-2, a fungal adhesin from Candida albicans

International Nuclear Information System (INIS)

Salgado, Paula S.; Yan, Robert; Rowan, Fiona; Cota, Ernesto

2011-01-01

Details of the expression and crystallization of the N-terminal fragment of Als9-2, an adhesin from the human commensal/pathogenic fungus C. albicans, are reported. Preliminary analysis of the collected X-ray data is also discussed. Candida albicans is a common human fungal commensal that can also cause a range of infections from skin/mucosal ‘thrush’ to severe systemic candidiasis. Adherence to host cells is one of the key determinants of Candida pathogenesis. The Als family of surface proteins has been implicated in adhesion of C. albicans, yet limited information has been published on the structure and mechanism of these fungal adhesins. The N-terminal region of these proteins has been shown to possess adhesive properties, making it a possible target for new therapeutic strategies. Recombinant NT-Als9-2 from C. albicans (residues 18–329) was overexpressed in Escherichia coli, purified and crystallized. Diffraction data were collected to 2.0 Å resolution. The crystals belonged to space group P2 1 2 1 2 1 , with unit-cell parameters a = 34.73, b = 68.71, c = 120.03 Å, α = β = γ = 90° and one molecule in the asymmetric unit. Platinum-derivatized crystals belonged to the same space group, with similar unit-cell parameters, although they were not completely isomorphous

Crystal surface analysis using matrix textural features classified by a Probabilistic Neural Network

International Nuclear Information System (INIS)

Sawyer, C.R.; Quach, V.T.; Nason, D.; van den Berg, L.

1991-01-01

A system is under development in which surface quality of a growing bulk mercuric iodide crystal is monitored by video camera at regular intervals for early detection of growth irregularities. Mercuric iodide single crystals are employed in radiation detectors. A microcomputer system is used for image capture and processing. The digitized image is divided into multiple overlappings subimage and features are extracted from each subimage based on statistical measures of the gray tone distribution, according to the method of Haralick [1]. Twenty parameters are derived from each subimage and presented to a Probabilistic Neural Network (PNN) [2] for classification. This number of parameters was found to be optimal for the system. The PNN is a hierarchical, feed-forward network that can be rapidly reconfigured as additional training data become available. Training data is gathered by reviewing digital images of many crystals during their growth cycle and compiling two sets of images, those with and without irregularities. 6 refs., 4 figs

Crystal-field energy level analysis for Nd3+ ions at the low symmetry C1 site in [Nd(hfa)4(H2O)](N(C2H5)4) single crystals

International Nuclear Information System (INIS)

Mech, Agnieszka; Gajek, Zbigniew; Karbowiak, Miroslaw; Rudowicz, Czeslaw

2008-01-01

Optical absorption measurements of Nd 3+ ions in single crystals of [Nd(hfa) 4 (H 2 O)](N(C 2 H 5 ) 4 ) (hfa = hexafluoroacetyloacetonate), denoted Nd(hfa) for short, have been carried out at 4.2 and 298 K. This compound crystallizes in the monoclinic system (space group P 2 1 /n). Each Nd ion is coordinated to eight oxygen atoms that originate from the hexafluoroacetylacetonate ligands and one oxygen atom from the water molecule. A total of 85 experimental crystal-field (CF) energy levels arising from the Nd 3+ (4f 3 ) electronic configuration were identified in the optical spectra and assigned. A three-step CF analysis was carried out in terms of a parametric Hamiltonian for the actual C 1 symmetry at the Nd 3+ ion sites. In the first step, a total of 27 CF parameters (CFPs) in the Wybourne notation B kq , admissible by group theory, were determined in a preliminary fitting constrained by the angular overlap model predictions. The resulting CFP set was reduced to 24 specific independent CFPs using appropriate standardization transformations. Optimizations of the second-rank CFPs and extended scanning of the parameter space were employed in the second step to improve reliability of the CFP sets, which is rather a difficult task in the case of no site symmetry. Finally, seven free-ion parameters and 24 CFPs were freely varied, yielding an rms deviation between the calculated energy levels and the 85 observed ones of 11.1 cm -1 . Our approach also allows prediction of the energy levels of Nd 3+ ions that are hidden in the spectral range overlapping with strong ligand absorption, which is essential for understanding the inter-ionic energy transfer. The orientation of the axis system associated with the fitted CF parameters w.r.t. the crystallographic axes is established. The procedure adopted in our calculations may be considered as a general framework for analysis of CF levels of lanthanide ions at low (triclinic) symmetry sites

Crystal-field energy level analysis for Nd(3+) ions at the low symmetry C(1) site in [Nd(hfa)(4)(H(2)O)](N(C(2)H(5))(4)) single crystals.

Science.gov (United States)

Mech, Agnieszka; Gajek, Zbigniew; Karbowiak, Mirosław; Rudowicz, Czesław

2008-09-24

Optical absorption measurements of Nd(3+) ions in single crystals of [Nd(hfa)(4)(H(2)O)](N(C(2)H(5))(4)) (hfa = hexafluoroacetyloacetonate), denoted Nd(hfa) for short, have been carried out at 4.2 and 298 K. This compound crystallizes in the monoclinic system (space group P 2(1)/n). Each Nd ion is coordinated to eight oxygen atoms that originate from the hexafluoroacetylacetonate ligands and one oxygen atom from the water molecule. A total of 85 experimental crystal-field (CF) energy levels arising from the Nd(3+) (4f(3)) electronic configuration were identified in the optical spectra and assigned. A three-step CF analysis was carried out in terms of a parametric Hamiltonian for the actual C(1) symmetry at the Nd(3+) ion sites. In the first step, a total of 27 CF parameters (CFPs) in the Wybourne notation B(kq), admissible by group theory, were determined in a preliminary fitting constrained by the angular overlap model predictions. The resulting CFP set was reduced to 24 specific independent CFPs using appropriate standardization transformations. Optimizations of the second-rank CFPs and extended scanning of the parameter space were employed in the second step to improve reliability of the CFP sets, which is rather a difficult task in the case of no site symmetry. Finally, seven free-ion parameters and 24 CFPs were freely varied, yielding an rms deviation between the calculated energy levels and the 85 observed ones of 11.1 cm(-1). Our approach also allows prediction of the energy levels of Nd(3+) ions that are hidden in the spectral range overlapping with strong ligand absorption, which is essential for understanding the inter-ionic energy transfer. The orientation of the axis system associated with the fitted CF parameters w.r.t. the crystallographic axes is established. The procedure adopted in our calculations may be considered as a general framework for analysis of CF levels of lanthanide ions at low (triclinic) symmetry sites.

Crystal-field energy level analysis for Nd3+ ions at the low symmetry C1 site in [Nd(hfa)4(H2O)](N(C2H5)4) single crystals

Science.gov (United States)

Mech, Agnieszka; Gajek, Zbigniew; Karbowiak, Mirosław; Rudowicz, Czesław

2008-09-01

Optical absorption measurements of Nd3+ ions in single crystals of [Nd(hfa)4(H2O)](N(C2H5)4) (hfa = hexafluoroacetyloacetonate), denoted Nd(hfa) for short, have been carried out at 4.2 and 298 K. This compound crystallizes in the monoclinic system (space group P 21/n). Each Nd ion is coordinated to eight oxygen atoms that originate from the hexafluoroacetylacetonate ligands and one oxygen atom from the water molecule. A total of 85 experimental crystal-field (CF) energy levels arising from the Nd3+ (4f3) electronic configuration were identified in the optical spectra and assigned. A three-step CF analysis was carried out in terms of a parametric Hamiltonian for the actual C1 symmetry at the Nd3+ ion sites. In the first step, a total of 27 CF parameters (CFPs) in the Wybourne notation Bkq, admissible by group theory, were determined in a preliminary fitting constrained by the angular overlap model predictions. The resulting CFP set was reduced to 24 specific independent CFPs using appropriate standardization transformations. Optimizations of the second-rank CFPs and extended scanning of the parameter space were employed in the second step to improve reliability of the CFP sets, which is rather a difficult task in the case of no site symmetry. Finally, seven free-ion parameters and 24 CFPs were freely varied, yielding an rms deviation between the calculated energy levels and the 85 observed ones of 11.1 cm-1. Our approach also allows prediction of the energy levels of Nd3+ ions that are hidden in the spectral range overlapping with strong ligand absorption, which is essential for understanding the inter-ionic energy transfer. The orientation of the axis system associated with the fitted CF parameters w.r.t. the crystallographic axes is established. The procedure adopted in our calculations may be considered as a general framework for analysis of CF levels of lanthanide ions at low (triclinic) symmetry sites.

Hydrothermally grown zeolite crystals

International Nuclear Information System (INIS)

Durrani, S.K.; Qureshi, A.H.; Hussain, M.A.; Qazi, N.K.

2009-01-01

The aluminium-deficient and ferrosilicate zeolite-type materials were synthesized by hydrothermal process at 150-170 degree C for various periods of time from the mixtures containing colloidal reactive silica, sodium aluminate, sodium hydroxide, iron nitrate and organic templates. Organic polycation templates were used as zeolite crystal shape modifiers to enhance relative growth rates. The template was almost completely removed from the zeolite specimens by calcination at 550 degree C for 8h in air. Simultaneous thermogravimetric (TG) and differential thermal analysis (DTA) was performed to study the removal of water molecules and the amount of organic template cations occluded inside the crystal pore of zeolite framework. The 12-13% weight loss in the range of (140-560 degree C) was associated with removal of the (C/sub 3/H/sub 7/)/sub 4/ N+ cation and water molecules. X-ray diffraction (XRD) analysis and scanning electron microscope (SEM) techniques were employed to study the structure, morphology and surface features of hydrothermally grown aluminium-deficient and ferrosilicate zeolite-type crystals. In order to elucidate the mode of zeolite crystallization the crystallinity and unit cell parameters of the materials were determined by XRD, which are the function of Al and Fe contents of zeolites. (author)

Effect of γ-irradiation on the lattice parameter and colour centre concentration in pure Ca2+, Sr2+ and Eu2+ doped KCl crystals

International Nuclear Information System (INIS)

Damm, J.Z.; Stepien-Damm, J.

1980-01-01

The changes of lattice parameter and colour centre concentration are examined in KCl crystals (both pure and Me 2+ -doped) irradiated by γ-rays at room temperature. For the pure crystals the relative volume change vs. F-centre concentration plot reveals the presence of two stages, one ascribed to the introduction of colour centre pairs (or F centres only) and other to the generation of new dislocations (or new dislocations with trapped-hole centres). In Me 2+ doped crystals the lattice expansion bears a complex character (in the initial irradiation stage a transient maximum appears). Additional anomaly appears in Eu 2+ KCl in the high-dose range where in spite of a distinct F-centre concentration drop a marked raise of the lattice parameter is observed. (author)

Crystals structure of Na3Li(TiF6)2

International Nuclear Information System (INIS)

Popov, D.Yu.; Antokhina, T.F.; Gerasimenko, A.V.; Kajdalova, T.A.; Sergienko, V.I.

2004-01-01

Crystals of Na 3 Li(TiF 6 ) 2 (1) were synthesized in aqueous solution and characterized by the elementary and X-ray phase analysis methods. According to X-ray diffraction analysis data compound 1 is crystallized in a tetragonal crystal system with the following parameters: a=5.130(1), c=18.046(4) A, Z=2, space group P4-bar2 1 c. Alternating layers on the basis of dimers made up by octahedrons of TiF 6 and Na(1)F 6 constitute the frame of compound 1 crystal structure. The dimer layers are joined in a continuous frame by Na(2) and Li cations. Coordination polyhedron of Li atom is tetrahedron (Li-F 1.898(3) A) [ru

Use of three-dimensional parameters in the analysis of crystal structures under compression

DEFF Research Database (Denmark)

Balic Zunic, Tonci

2007-01-01

. For a complete understanding of structural changes, the behaviour of all coordination polyhedra plus the voids that separate them must be investigated. The structural voids in a framework are identified by a Voronoi tessellation. It can be performed e.g. on the anionic framework alone to find the centres...... information. Accurate determination of atomic coordinations is difficult in cases where a clear bond gap does not exist. In such instances the most reliable existing method is the determination of atomic domains in electron density, which can be performed even for experimental high-pressure crystal structure...

Growth Aspects, Structural and Optical Properties of 2-aminopyridinium 2,4 Dinitrophenolate Single Crystal

Directory of Open Access Journals (Sweden)

S. Reena Devi

2017-06-01

Full Text Available Organic single crystal of 2-aminopyridinium 2,4-dinitrophenolate single crystal was grown by slow evaporation technique. The cell parameters and space group (P were determined from single X-ray diffraction analysis. HRXRD studies ascertained the crystalline quality. UV-Visible and PL spectral studies revealed the emission in red region, transparency (75% cutoff wavelength around 440 nm respectively. The laser damage threshold of grown crystal was estimated by using Nd:YAG laser beam and these results were mutually related with specific heat capacity of the grown crystal. The third-order nonlinear optical parameters were estimated by Z-scan technique which is useful for optical applications.

Growth and microtopographic study of CuInSe{sub 2} single crystals

Energy Technology Data Exchange (ETDEWEB)

Chauhan, Sanjaysinh M.; Chaki, Sunil, E-mail: sunilchaki@yahoo.co.in; Deshpande, M. P. [Department of Physics, Sardar Patel University, Vallabh Vidyanagar, Gujarat - 388120 (India); Tailor, J. P. [Applied Physics Department, S.V.N.I.T., Surat, Gujarat - 395007 (India)

2016-05-23

The CuInSe{sub 2} single crystals were grown by chemical vapour transport (CVT) technique using iodine as transporting agent. The elemental composition of the as-grown CuInSe{sub 2} single crystals was determined by energy dispersive analysis of X-ray (EDAX). The unit cell crystal structure and lattice parameters were determined by X-ray diffraction (XRD) technique. The surface microtopographic study of the as-grown CuInSe{sub 2} single crystals surfaces were done to study the defects, growth mechanism, etc. of the CVT grown crystals.

Cloning, expression, purification, crystallization and preliminary X-ray analysis of a fructokinase from Vibrio cholerae O395

International Nuclear Information System (INIS)

Paul, Rakhi; Nath, Seema; Sen, Udayaditya

2012-01-01

A fructokinase from V. cholerae O395 has been cloned, expressed, purified and crystallized in the apo form; the crystals belonged to the orthorhombic space group P2 1 2 1 2 and diffracted to 2.45 Å resolution. Fructokinase with ADP and fructose bound has also been crystallized and the crystals diffracted to a resolution of 1.75 Å. Fructokinase (FK), one of the crucial enzymes for sugar metabolism in bacterial systems, catalyses the unidirectional phosphorylation reaction from fructose to fructose 6-phosphate, thereby allowing parallel entry of fructose into glycolysis beside glucose. The cscK gene from Vibrio cholerae O395 coding for the enzyme FK has been cloned, overexpressed in Escherichia coli BL21 (DE3) and purified using Ni–NTA affinity chromatography. Crystals of V. cholerae FK (Vc-FK) and its cocrystal with fructose, adenosine diphosphate (ADP) and Mg 2+ were grown in the presence of polyethylene glycol 6000 and diffracted to 2.45 and 1.75 Å resolution, respectively. Analysis of the diffraction data showed that both crystal forms have symmetry consistent with space group P2 1 2 1 2, but with different unit-cell parameters. Assuming the presence of two molecules in the asymmetric unit, the Matthews coefficient for the apo Vc-FK crystals was estimated to be 2.4 Å 3 Da −1 , which corresponds to a solvent content of 48%. The corresponding values for the ADP- and sugar-bound Vc-FK crystals were 2.1 Å 3 Da −1 and 40%, respectively, assuming the presence of one molecule in the asymmetric unit

Crystallization and preliminary X-ray diffraction analysis of PAT, an acetyltransferase from Sulfolobus solfataricus

International Nuclear Information System (INIS)

Cho, Ching-Chang; Luo, Ching-Wei; Hsu, Chun-Hua

2008-01-01

PAT, an acetyltransferase from the archaeon S. solfataricus that specifically acetylates the chromatin protein Alba, was expressed, purified and crystallized. PAT is an acetyltransferase from the archaeon Sulfolobus solfataricus that specifically acetylates the chromatin protein Alba. The enzyme was expressed, purified and subsequently crystallized using the sitting-drop vapour-diffusion technique. Native diffraction data were collected to 1.70 Å resolution on the BL13C1 beamline of NSRRC from a flash-frozen crystal at 100 K. The crystals belonged to space group P2 1 2 1 2 1 , with unit-cell parameters a = 44.30, b = 46.59, c = 68.39 Å

Effect of cobalt on microstructural parameters and mechanical properties of Ni-base single crystal superalloys

International Nuclear Information System (INIS)

Suzuki, Takanobu; Imai, Hachiro; Yokokawa, Tadaharu; Kobayashi, Toshiharu; Koizumi, Yutaka; Harada, Hiroshi

2007-01-01

The alloying effect of Cobalt (Co) to microstructural parameters and mechanical properties, such as partitioning ratios of alloying elements and creep strength, of Re-bearing Ni-base single crystal superalloys have been investigated. The second generation single crystal superalloys, TMS-82+, Ni-7.8Co-4.9Cr-1.9Mo-8.7W-5.3Al-6.0Ta-2.4Re-0.1Hf, in mass% (8Co) was compared to a Co-free (0Co) and 15 mass% Co (15Co) alloy which had the same chemical composition as TMS-82+ except that Co was changed. It was shown that the partitioning ratios of alloying elements trend to k(=X γ /X' γ )=1, as the content of Co was increased. Furthermore, it was found that there was suitable content of Co for the creep strength under various temperature-stress conditions. (author)

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.

Crystal growth and mechanical hardness of In{sub 2}Se{sub 2.7}Sb{sub 0.3} single crystal

Energy Technology Data Exchange (ETDEWEB)

Patel, Piyush, E-mail: piyush-patel130@yahoo.com; Vyas, S. M., E-mail: s-m-vyas-gu@hotmail.com; Patel, Vimal; Pavagadhi, Himanshu [Department of Physics, School of Science, Gujarat University, Ahmedabad, Gujarat, India-380009 (India); Solanki, Mitesh [panditdindayal Petroleum University, Gandhinagar. Gujarat (India); Jani, Maunik P. [BITS Edu Campus, Varnama, Vadodara, Gujarat (India)

2015-08-28

The III-VI compound semiconductors is important for the fabrication of ionizing radiation detectors, solid-state electrodes, and photosensitive heterostructures, solar cell and ionic batteries. In this paper, In{sub 2}Se{sub 2.7} Sb{sub 0.3} single crystals were grown by the Bridgman method with temperature gradient of 60 °C/cm and the growth velocity 0.5cm/hr. The as-grown crystals were examined under the optical microscope for surface study, a various growth features observed on top free surface of the single crystal which is predominant of layers growth mechanism. The lattice parameters of as-grown crystal was determined by the XRD analysis. A Vickers’ projection microscope were used for the study of microhardness on the as-cleaved, cold-worked and annealed samples of the crystals, the results were discussed, and reported in detail.

Preparation, crystallization and preliminary X-ray analysis of YjcG protein from Bacillus subtilis

International Nuclear Information System (INIS)

Li, Dan; Chan, Chiomui; Liang, Yu-He; Zheng, Xiaofeng; Li, Lanfen; Su, Xiao-Dong

2005-01-01

B. subtilis YjcG protein was expressed, purified and crystallized. A complete diffraction data set was collected at BSRF beamline 3W1A and processed to 2.3 Å resolution. Bacillus subtilis YjcG is a functionally uncharacterized protein with 171 residues that has no structural homologue in the Protein Data Bank. However, it shows sequence homology to bacterial and archaeal 2′–5′ RNA ligases. In order to identify its exact function via structural studies, the yjcG gene was amplified from B. subtilis genomic DNA and cloned into the expression vector pET21-DEST. The protein was expressed in a soluble form in Escherichia coli and was purified to homogeneity. Crystals suitable for X-ray analysis were obtained that diffracted to 2.3 Å and belonged to space group C2, with unit-cell parameters a = 99.66, b = 73.93, c = 61.77 Å, β = 113.56°

Alternative crystal field parameters for rare-earth ions obtained from various techniques: IV. Comparative analysis of crystal field parameters obtained from inelastic neutron scattering and related studies of RE ions (RE = Er{sup 3+}, Ho{sup 3+}, Nd{sup 3+}, Pr{sup 3+}) in REBa{sub 2}Cu{sub 3}O{sub 7-{delta}} high-T{sub c} superconductors

Energy Technology Data Exchange (ETDEWEB)

Rudowicz, Czeslaw, E-mail: crudowicz@zut.edu.pl [Modeling in Spectroscopy Group, Institute of Physics, Faculty of Mechanical Engineering and Mechatronics, West Pomeranian University of Technology, Szczecin, al. Piastow 48, 70-311 Szczecin (Poland); Lewandowska, Monika [Modeling in Spectroscopy Group, Institute of Physics, Faculty of Mechanical Engineering and Mechatronics, West Pomeranian University of Technology, Szczecin, al. Piastow 48, 70-311 Szczecin (Poland)

2012-11-05

Highlights: Black-Right-Pointing-Pointer Orthorhombic crystal field parameters (CFPs) for RE3{sup +} in REBa{sub 2}Cu{sub 3}O{sub 7-{delta}} studied. Black-Right-Pointing-Pointer Comparative analysis of CFP sets for Er{sup 3+}, Ho{sup 3+}, Nd{sup 3+}, and Pr{sup 3+} ions performed. Black-Right-Pointing-Pointer Aspects related to CFP standardization considered. Black-Right-Pointing-Pointer Several problems identified due to comparative CFP analysis clarified. Black-Right-Pointing-Pointer Correct comparison of different CFP sets must be based on standardization. - Abstract: This is fourth paper in a series devoted to reanalysis of the non-standard and standard crystal-field (CF) parameter (CFP) sets obtained from various experimental techniques and theoretical models for trivalent rare-earth (RE) ions in high-critical-temperature (high-T{sub c}) superconductors and related systems. In this paper the experimental orthorhombic CFPs, obtained mostly by inelastic neutron scattering techniques and to a lesser extent by magnetic susceptibility and specific heat measurements as well as the respective theoretical CFPs for Er{sup 3+}, Ho{sup 3+}, Nd{sup 3+}, and Pr{sup 3+} ions in REBa{sub 2}Cu{sub 3}O{sub 7-{delta}} compounds, are considered. Several problems identified due to the comparative CFP analysis: (i) confusing notations used for operators and CFPs, (ii) different scaling factors and units used for CFPs, and (iii) lack of clear definitions of the axis systems used to express CFPs, were clarified. For each ion studied the available experimental and theoretical CFP sets are analyzed, standardized, and presented in a unified way. The large number of CFP sets prevents calculation of the five additional alternative sets for each originally reported CFP set. Instead, the alternative CFP sets are determined using the package CST for an average set calculated for selected compatible sets for each ion. These alternative CFP sets may be utilized in the multiple correlated

Crystal structure and magnetic susceptibility of UOSe single crystals

International Nuclear Information System (INIS)

Kaczorowski, D.; Muenster Univ.; Poettgen, R.; Jeitschko, W.; Gajek, Z.; Zygmunt, A.

1993-01-01

The crystal structure and magnetic susceptibility behaviour of UOSe single crystals have been studied. UOSe crystalizes in the tetragonal PbFC1-type structure (space group P4/nmm) with the lattice parameters: a = 390.38(5) pm and c = 698.05(9) pm. It orders antiferromagnetically at T N =100±2 K and exhibits a very strong anisotropy in the susceptibility vs temperature variation. The magnetic and thermodynamic properties of UOSe are successfully interpreted in the framework of a perturbative ab initio crystal field approach. (Author)

Crystal structure and magnetic susceptibility of UOSe single crystals

Energy Technology Data Exchange (ETDEWEB)

Kaczorowski, D. (Polish Academy of Sciences, Wroclaw (Poland). Inst. for Low Temperature and Structure Research Muenster Univ. (Germany). Anorganisch-Chemisches Inst.); Poettgen, R.; Jeitschko, W. (Muenster Univ. (Germany). Anorganisch-Chemisches Inst.); Gajek, Z.; Zygmunt, A. (Polish Academy of Sciences, Wroclaw (Poland). Inst. for Low Temperature and Structure Research)

1993-01-01

The crystal structure and magnetic susceptibility behaviour of UOSe single crystals have been studied. UOSe crystalizes in the tetragonal PbFC1-type structure (space group P4/nmm) with the lattice parameters: a = 390.38(5) pm and c = 698.05(9) pm. It orders antiferromagnetically at T[sub N]=100[+-]2 K and exhibits a very strong anisotropy in the susceptibility vs temperature variation. The magnetic and thermodynamic properties of UOSe are successfully interpreted in the framework of a perturbative ab initio crystal field approach. (Author).

Unifying the crystallization behavior of hexagonal and square crystals with the phase-field-crystal model

International Nuclear Information System (INIS)

Yang Tao; Chen Zheng; Zhang Jing; Wang Yongxin; Lu Yanli

2016-01-01

By employing the phase-field-crystal models, the atomic crystallization process of hexagonal and square crystals is investigated with the emphasis on the growth mechanism and morphological change. A unified regime describing the crystallization behavior of both crystals is obtained with the thermodynamic driving force varying. By increasing the driving force, both crystals (in the steady-state) transform from a faceted polygon to an apex-bulged polygon, and then into a symmetric dendrite. For the faceted polygon, the interface advances by a layer-by-layer (LL) mode while for the apex-bulged polygonal and the dendritic crystals, it first adopts the LL mode and then transits into the multi-layer (ML) mode in the later stage. In particular, a shift of the nucleation sites from the face center to the area around the crystal tips is detected in the early growth stage of both crystals and is rationalized in terms of the relation between the crystal size and the driving force distribution. Finally, a parameter characterizing the complex shape change of square crystal is introduced. (paper)

Overproduction, crystallization and preliminary X-ray analysis of the putative l-ascorbate-6-phosphate lactonase UlaG from Escherichia coli

International Nuclear Information System (INIS)

Garces, Fernando; Fernández, Francisco J.; Pérez-Luque, Rosa; Aguilar, Juan; Baldomà, Laura; Coll, Miquel; Badía, Josefa; Vega, M. Cristina

2007-01-01

UlaG, the putative l-ascorbate-6-phosphate lactonase encoded by the ulaG gene from the utilization of l-ascorbate regulon in E. coli, has been cloned, overexpressed, purified using standard chromatographic techniques and crystallized in a monoclinic space group. Crystals were obtained by the sitting-drop vapour-diffusion method at 293 K. A data set diffracting to 3 Å resolution was collected from a single crystal at 100 K. UlaG, the putative l-ascorbate-6-phosphate lactonase encoded by the ulaG gene from the utilization of l-ascorbate regulon in Escherichia coli, has been cloned, overexpressed, purified using standard chromatographic techniques and crystallized. Crystals were obtained by sitting-drop vapour diffusion at 293 K. Preliminary X-ray diffraction analysis revealed that the UlaG crystals belonged to the monoclinic space group C2, with unit-cell parameters a = 104.52, b = 180.69, c = 112.88 Å, β = 103.26°. The asymmetric unit is expected to contain six copies of UlaG, with a corresponding volume per protein weight of 2.16 Å 3 Da −1 and a solvent content of 43%

Effect of an azo dye (DR1) on the dielectric parameters of a nematic liquid crystal system

International Nuclear Information System (INIS)

Ozder, S.; Okutan, M.; Koeysal, O.; Goektas, H.; San, S.E.

2007-01-01

The dielectric parameters and relaxation properties of azo dye (DR1) doped E7 and pure E7 liquid crystal (LC) have been investigated in a wide frequency range of 10 k-10 MHz through the dielectric spectroscopy method at room temperature. Dielectric anisotropy (Δε) property of the LC changes from the positive type to negative type and dielectric anisotropy values decrease with doping of DR1. The relaxation frequency f r of E7 and E7/DR1 LC was calculated by means of Cole-Cole plots. Influence of bias voltage on the dielectric parameters has also been investigated

Crystallization and preliminary X-ray analysis of a d-Ala:d-Ser ligase associated with VanG-type vancomycin resistance

International Nuclear Information System (INIS)

Weber, Patrick; Meziane-Cherif, Djalal; Haouz, Ahmed; Saul, Frederick A.; Courvalin, Patrice

2009-01-01

The VanG d-alanine:d-serine ligase was crystallized in complex with ADP and diffraction data were collected at 2.35 Å resolution. Acquired VanG-type resistance to vancomycin in Enterococcus faecalis BM4518 arises from inducible synthesis of peptidoglycan precursors ending in d-alanyl-d-serine, to which vancomycin exhibits low binding affinity. VanG, a d-alanine:d-serine ligase, catalyzes the ATP-dependent synthesis of the d-Ala-d-Ser dipeptide, which is incorporated into the peptidoglycan synthesis of VanG-type vancomycin-resistant strains. Here, the purification, crystallization and preliminary crystallographic analysis of VanG in complex with ADP are reported. The crystal belonged to space group P3 1 21, with unit-cell parameters a = b = 116.1, c = 177.2 Å, and contained two molecules in the asymmetric unit. A complete data set has been collected to 2.35 Å resolution from a single crystal under cryogenic conditions using synchrotron radiation

Optimization of the scintillation parameters of the lead tungstate crystals for their application in high precision electromagnetic calorimetry; Optimisation des parametres de scintillation des cristaux de tungstate de plomb pour leur application dans la calorimetrie electromagnetique de haute precision

Energy Technology Data Exchange (ETDEWEB)

Drobychev, G

2000-04-12

In the frame of this dissertation work scintillation properties of the lead tungstate crystals (PWO) and possibilities of their use were studied foreseeing their application for electromagnetic calorimetry in extreme radiation environment conditions of new colliders. The results of this work can be summarized in the following way. 1. A model of the scintillations origin in the lead tungstate crystals which includes processes influencing on the crystals radiation hardness and presence of slow components in scintillations was developed. 2. An analysis of the influences of the PWO scintillation properties changes on the parameters of the electromagnetic calorimeter was done. 3. Methods of the light collection from the large scintillation elements of complex shape made of the birefringent scintillation crystal with high refraction index and low light yield in case of signal registration by a photodetector with sensitive surface small in compare with the output face of scintillator were Studied. 4. Physical principles of the methodology of the scintillation crystals certification during their mass production foreseeing their installation into a calorimeter electromagnetic were developed. Correlations between the results of measurements of the PWO crystals parameters by different methods were found. (author)

Purification, crystallization and preliminary crystallographic analysis of deoxyuridine triphosphate nucleotidohydrolase from Arabidopsis thaliana

International Nuclear Information System (INIS)

Bajaj, Mamta; Moriyama, Hideaki

2007-01-01

The first crystallization of deoxyuridine triphosphate nucleotidohydrolase from plant, Arabidopsis thaliana, has been performed. An additive, taurine, was effective in producing the single crystal. The deoxyuridine triphosphate nucleotidohydrolase gene from Arabidopsis thaliana was expressed and the gene product was purified. Crystallization was performed by the hanging-drop vapour-diffusion method at 298 K using 2 M ammonium sulfate as the precipitant. X-ray diffraction data were collected to 2.2 Å resolution using Cu Kα radiation. The crystal belongs to the orthorhombic space group P2 1 2 1 2 1 , with unit-cell parameters a = 69.90, b = 70.86 Å, c = 75.55 Å. Assuming the presence of a trimer in the asymmetric unit, the solvent content was 30%, with a V M of 1.8 Å 3 Da −1

Expression, purification, crystallization and preliminary crystallographic analysis of MxiH, a subunit of the Shigella flexneri type III secretion system needle

International Nuclear Information System (INIS)

Deane, Janet E.; Cordes, Frank S.; Roversi, Pietro; Johnson, Steven; Kenjale, Roma; Picking, William D.; Picking, Wendy L.; Lea, Susan M.; Blocker, Ariel

2006-01-01

A monodisperse truncation mutant of MxiH, the subunit of the S. flexneri type III secretion system needle, has been crystallized. SeMet derivatives and a uranyl derivative have undergone preliminary crystallographic analysis. A monodisperse truncation mutant of MxiH, the subunit of the needle from the Shigella flexneri type III secretion system (TTSS), has been overexpressed and purified. Crystals were grown of native and selenomethionine-labelled MxiH CΔ5 and diffraction data were collected to 1.9 Å resolution. The crystals belong to space group C2, with unit-cell parameters a = 183.4, b = 28.1, c = 27.8 Å, β = 96.5°. An anomalous difference Patterson map calculated with the data from the SeMet-labelled crystals revealed a single peak on the Harker section v = 0. Inspection of a uranyl derivative also revealed one peak in the isomorphous difference Patterson map on the Harker section v = 0. Analysis of the self-rotation function indicates the presence of a twofold non-crystallographic symmetry axis approximately along a. The calculated Matthews coefficient is 1.9 Å 3 Da −1 for two molecules per asymmetric unit, corresponding to a solvent content of 33%

Crystallization and preliminary X-ray crystallographic analysis of human quinolinate phosphoribosyltransferase

International Nuclear Information System (INIS)

Kang, Gil Bu; Kim, Mun-Kyoung; Youn, Hyung-Seop; An, Jun Yop; Lee, Jung-Gyu; Park, Kyoung Ryoung; Lee, Sung Hang; Kim, Yongseong; Fukuoka, Shin-Ichi; Eom, Soo Hyun

2010-01-01

H. sapiens quinolinate phosphoribosyltransferase has been expressed, purified and crystallized. A diffraction data set has been collected and processed at 2.8 Å resolution. Quinolinate phosphoribosyltransferase (QPRTase) is a key NAD-biosynthetic enzyme which catalyzes the transfer of quinolinic acid to 5-phosphoribosyl-1-pyrophosphate, yielding nicotinic acid mononucleotide. Homo sapiens QPRTase (Hs-QPRTase) appeared as a hexamer during purification and the protein was crystallized. Diffraction data were collected and processed at 2.8 Å resolution. Native Hs-QPRTase crystals belonged to space group P2 1 , with unit-cell parameters a = 76.2, b = 137.1, c = 92.7 Å, β = 103.8°. Assuming the presence of six molecules in the asymmetric unit, the calculated Matthews coefficient is 2.46 Å 3 Da −1 , which corresponds to a solvent content of 49.9%

Optical and dielectric studies of KH2PO4 crystal influenced by organic ligand of citric acid and l-valine: A single crystal growth and comparative study

Directory of Open Access Journals (Sweden)

Mohd Anis

Full Text Available In the present study pure, citric acid (CA and l-valine (LV doped potassium dihydrogen phosphate (KDP crystals have been grown with the aim to investigate the nonlinear optical applications facilitated by UV–visible, third order nonlinear optical (TONLO and dielectric properties. The structural parameters of grown crystals have been confirmed by single crystal X-ray diffraction analysis. The enhancement in optical transparency of KDP crystal due to addition of CA and LV has been examined within 200–900 nm by means of UV–visible spectral analysis. In addition, the transmittance data have been used to evaluate the effect of dopants on reflectance, refractive index and extinction coefficient of grown crystals in the visible region. The Z-scan analysis has been performed at 632.8 nm to identify the nature of photoinduced nonlinear refraction and nonlinear absorption in doped KDP crystals. The influence of π-bonded ligand of dopant CA and LV on TONLO susceptibility (χ3, refractive index (n2 and absorption coefficient (β of KDP crystals has been evaluated to discuss laser assisted device applications. The decrease in dielectric constant and dielectric loss of KDP crystal due to addition of CA and LV has been explored using the temperature dependent dielectric studies. Keywords: Crystal growth, Nonlinear optical materials, UV–visible studies, Z-scan analysis, Dielectric studies

Crystallization and preliminary X-ray diffraction analysis of the fructofuranosidase from Schwanniomyces occidentalis

International Nuclear Information System (INIS)

Polo, Aitana; Álvaro-Benito, Miguel; Fernández-Lobato, María; Sanz-Aparicio, Julia

2009-01-01

The invertase from Schwanniomyces occidentalis has been expressed in Saccharomyces cerevisiae, purified and crystallized. The wild-type enzyme was also purified and crystallized and diffraction data were collected to 2.9 Å resolution. Schwanniomyces occidentalis invertase is an extracellular enzyme that releases β-fructose from the nonreducing termini of various β-d-fructofuranoside substrates. Its ability to produce 6-kestose by transglycosylation makes this enzyme an interesting research target for applications in industrial biotechnology. The enzyme has been expressed in Saccharomyces cerevisiae. Recombinant and wild-type forms, which showed different glycosylation patterns, were crystallized by vapour-diffusion methods. Although crystallization trials were conducted on both forms of the protein, crystals suitable for X-ray crystallographic analyses were only obtained from the wild-type enzyme. The crystals belonged to space group P2 1 2 1 2 1 , with unit-cell parameters a = 105.78, b = 119.49, c = 137.68 Å. A diffraction data set was collected using a synchrotron source. Self-rotation function and sedimentation-velocity experiments suggested that the enzyme was dimeric with twofold symmetry

Crystallization and preliminary X-ray analysis of the V domain of human nectin-2

International Nuclear Information System (INIS)

Qian, Xiaomin; Qi, Jianxun; Chu, Fuliang; Liu, Jun; Li, Qing; Yan, Jinghua

2009-01-01

Crystals of the V domain of human nectin-2 diffracted to 1.85 Å resolution and were monoclinic, belonging to space group P2 1 , with unit-cell parameters a = 52.3, b = 43.9, c = 56.1 Å, β = 118.2°. Nectin-2 belongs to a family of immunoglobulin-like cell adhesion molecules that are characterized by the presence of three immunoglobulin-like domains (V, C2 and C2) in the extracellular region. The V domain plays important roles in cell adhesion, NK cell activation and the entry of some herpesvirus. In this study, the V domain of human nectin-2 was expressed in Escherichia coli in the form of inclusion bodies, which were subsequently denatured and refolded. The soluble protein was crystallized using the hanging-drop vapour-diffusion method. The crystals diffracted to 1.85 Å resolution and belonged to space group P2 1 , with unit-cell parameters a = 52.3, b = 43.9, c = 56.1 Å, β = 118.2°

Purification, crystallization and preliminary X-ray diffraction analysis of human Gadd45γ

International Nuclear Information System (INIS)

Zhang, Wenzheng; Zhao, Mingzhuo; Li, Jianhui; Li, Xuemei; Zeng, ZongHao; Rao, Zihe

2008-01-01

The human Gadd45γ protein has been crystallized as a prelude towards determination of its three-dimensional structure by X-ray crystallography. Gadd45, MyD118 and CR6 (also termed Gadd45α, Gadd45β and Gadd45γ, respectively) comprise a family of proteins that play important roles in negative growth control, maintenance of genomic stability, DNA repair, cell-cycle control and apoptosis. Recombinant human Gadd45γ and its selenomethionine derivative were expressed in an Escherichia coli expression system and purified; they were then crystallized using the hanging-drop vapour-diffusion method. Diffraction-quality crystals were grown at 291 K using PEG 3350 as precipitant. Using synchrotron radiation, the best diffraction data were collected to 2.3 Å resolution for native crystals at 100 K; selenomethionyl derivative data were collected to 3.3 Å resolution. All the crystals belonged to space group I2 1 3, with approximate unit-cell parameters a = b = c = 126 Å

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

Energy Technology Data Exchange (ETDEWEB)

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

2013-07-15

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

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

International Nuclear Information System (INIS)

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

2013-01-01

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

Crystallization and preliminary crystallographic analysis of maganese(II)-dependent 2,3-dihydroxybiphenyl 1,2-dioxygenase from Bacillus sp. JF8

International Nuclear Information System (INIS)

Senda, Miki; Hatta, Takashi; Kimbara, Kazuhide; Senda, Toshiya

2010-01-01

A thermostable manganese(II)-dependent 2,3-dihydroxybiphenyl-1,2-dioxygenase derived from Bacillus sp. JF8 was crystallized in two forms using the sitting-drop vapour-diffusion method. Both crystals diffracted to approximately 1.3 Å resolution. A thermostable manganese(II)-dependent 2,3-dihydroxybiphenyl-1,2-dioxygenase derived from Bacillus sp. JF8 was crystallized. The initial screening for crystallization was performed by the sitting-drop vapour-diffusion method using a crystallization robot, resulting in the growth of two crystal forms. The first crystal belonged to space group P1, with unit-cell parameters a = 62.7, b = 71.4, c = 93.6 Å, α = 71.2, β = 81.0, γ = 64.0°, and diffracted to 1.3 Å resolution. The second crystal belonged to space group I222, with unit-cell parameters a = 74.2, b = 90.8, c = 104.3 Å, and diffracted to 1.3 Å resolution. Molecular-replacement trials using homoprotocatechuate 2,3-dioxygenase from Arthrobacter globiformis (28% amino-acid sequence identity) as a search model provided a satisfactory solution for both crystal forms

Research on crystal growth by using pressure as a control parameter; Atsuryoku seigyo ni yoru kessho seicho ni kansuru kenkyu

Energy Technology Data Exchange (ETDEWEB)

NONE

1997-10-31

This research project aims to establish a technique for crystal growth using pressure as a principal control parameter, and combining it with a microgravity condition, to develop a novel process material fabrication. Since the solubility of materials depends on pressure, it is possible to control a supersaturated condition for crystal growth by changing pressure. The growth condition can be controlled precisely, which is not possible by conventional methods that vary temperature and other factors. On the other hand, because a concentration diffusing field is formed autonomically around crystals in association with their growth, density convection is generated under gravity as a result of difference in the concentrations, making the growth conditions severely complex and uncontrollable. Ideal crystal growth condition control may be possible if the pressure control is performed under micro-gravity by which generation of the density convection can be suppressed. Realization has been achieved on in-situ observation by using high-magnification microscope which uses a diamond anvil cell, development of a hydraulic type optic pressure cell, and a high- speed crystal growing technology by means of pressure control utilizing the cell. New findings were also obtained on effects of pressure on crystal forms, and the pressure induced solid phase transfer mechanism. 67 refs., 49 figs., 3 tabs.

Crystal growth, characterization and theoretical studies of 4-aminopyridinium picrate

Science.gov (United States)

Aditya Prasad, A.; Muthu, K.; Rajasekar, M.; Meenatchi, V.; Meenakshisundaram, S. P.

2015-01-01

Single crystals of 4-aminopyridinium picrate (APP) were grown by slow evaporation of a mixed solvent system methanol-acetone (1:1, v/v) containing equimolar quantities of 4-aminopyridine and picric acid. Structure is elucidated by single crystal XRD analysis and the crystal belongs to monoclinic system with four molecules in the unit cell (space group P21/c) and the cell parameter values are, a = 8.513 Å (±0.015), b = 11.33 Å (±0.02), c = 14.33 Å (±0.03) and β = 104.15° (±0.019), V = 1340 A3 (±6) with refined R factors R1 = 0.0053 and wR2 = 0.0126. The electron density mapping is interpreted to find coordinates for each atom in the crystallized molecules. The various functional groups present in the molecule are confirmed by FT-IR analysis. UV-visible spectral analysis was used to determine the band gap energy of 4-aminopyridinium picrate. Powder X-ray diffraction pattern reveals the crystallinity of the as-grown crystal and it closely resembles the simulated XRD from the single crystal XRD analysis. Scanning electron microscopy reveals the surface morphology of the grown crystal. Optimized geometry is derived by Hartree-Fock theory calculations and the first-order molecular hyperpolarizability (β), theoretically calculated bond length, bond angles and excited state energy from theoretical UV-vis spectrum were estimated.

Crystallization and preliminary X-ray analysis of CooA from Carboxydothermus hydrogenoformans

International Nuclear Information System (INIS)

Komori, Hirofumi; Satomoto, Kensuke; Ueda, Yasufumi; Shibata, Naoki; Inagaki, Sayaka; Yoshioka, Shiro; Aono, Shigetoshi; Higuchi, Yoshiki

2006-01-01

CooA from C. hydrogenoformans has been crystallized by the vapour-diffusion method using polyethylene glycol as a precipitant. The crystal diffracted to 2.3 Å resolution. CooA, a homodimeric haem-containing protein, is responsible for transcriptional regulation in response to carbon monoxide (CO). It has a b-type haem as a CO sensor. Upon binding CO to the haem, CooA binds promoter DNA and activates expression of genes for CO metabolism. CooA from Carboxydothermus hydrogenoformans has been overexpressed in Escherichia coli, purified and crystallized by the vapour-diffusion method. The crystal belongs to space group P2 1 , with unit-cell parameters a = 61.8, b = 94.7, c = 92.8 Å, β = 104.8°. The native and anomalous difference Patterson maps indicated that two CooA dimers are contained in the asymmetric unit and are related by a translational symmetry almost parallel to the c axis

Crystallization and preliminary X-ray analysis of cecropin B from Bombyx mori

International Nuclear Information System (INIS)

Liu, Zhongyuan; Zhou, Qiangjun; Mao, Xinfang; Zheng, Xiangdong; Guo, Jiubiao; Zhang, Fuchun; Wen, Tingyi; Pang, Hai

2010-01-01

Cecropin B derived from the hemolymph of Bombyx mori has been crystallized by the hanging-drop vapour-diffusion method. The crystal diffracted to 1.43 Å resolution using X-ray radiation. Cecropin B is a 37-residue cationic antimicrobial peptide derived from the haemolymph of Bombyx mori. The precise mechanism by which cecropins exert their antimicrobial and cytolytic activities is not well understood. Crystals of cecropin B were obtained by the hanging-drop vapour-diffusion method using polyethylene glycol as a precipitant at 289 K. The crystal diffracted to 1.43 Å resolution using X-ray radiation and belonged to the orthorhombic space group P1, with unit-cell parameters a = 15.08, b = 22.75, c = 30.20 Å, α = 96.9, β = 103.1, γ = 96.5°. The asymmetric unit contained only one molecule of cecropin B, with a calculated Matthews coefficient of 2.48 Å 3 Da −1 and a solvent content of 50.4%

Optics of globular photonic crystals

International Nuclear Information System (INIS)

Gorelik, V S

2007-01-01

The results of experimental and theoretical studies of the optical properties of globular photonic crystals - new physical objects having a crystal structure with the lattice period exceeding considerably the atomic size, are presented. As globular photonic crystals, artificial opal matrices consisting of close-packed silica globules of diameter ∼200 nm were used. The reflection spectra of these objects characterising the parameters of photonic bands existing in these crystals in the visible spectral region are presented. The idealised models of the energy band structure of photonic crystals investigated in the review give analytic dispersion dependences for the group velocity and the effective photon mass in a globular photonic crystal. The characteristics of secondary emission excited in globular photonic crystals by monochromatic and broadband radiation are presented. The results of investigations of single-photon-excited delayed scattering of light observed in globular photonic crystals exposed to cw UV radiation and radiation from a repetitively pulsed copper vapour laser are presented. The possibilities of using globular photonic crystals as active media for lasing in different spectral regions are considered. It is proposed to use globular photonic crystals as sensitive sensors in optoelectronic devices for molecular analysis of organic and inorganic materials by the modern methods of laser spectroscopy. The results of experimental studies of spontaneous and stimulated globular scattering of light are discussed. The conditions for observing resonance and two-photon-excited delayed scattering of light are found. The possibility of accumulation and localisation of the laser radiation energy inside a globular photonic crystal is reported. (review)

Computational strain gradient crystal plasticity

DEFF Research Database (Denmark)

Niordson, Christian Frithiof; Kysar, Jeffrey W.

2014-01-01

A numerical method for viscous strain gradient crystal plasticity theory is presented, which incorporates both energetic and dissipative gradient effects. The underlying minimum principles are discussed as well as convergence properties of the proposed finite element procedure. Three problems...... of plane crystal plasticity are studied: pure shear of a single crystal between rigid platens as well as plastic deformation around cylindrical voids in hexagonal close packed and face centered cubic crystals. Effective in-plane constitutive slip parameters for plane strain deformation of specifically...... oriented face centered cubic crystals are developed in terms of the crystallographic slip parameters. The effect on geometrically necessary dislocation structures introduced by plastic deformation is investigated as a function of the ratio of void radius to plasticity length scale....

Thermal-capillary analysis of Czochralski and liquid encapsulated Czochralski crystal growth. II - Processing strategies

Science.gov (United States)

Derby, J. J.; Brown, R. A.

1986-01-01

The pseudosteady-state heat transfer model developed in a previous paper is augmented with constraints for constant crystal radius and melt/solid interface deflection. Combinations of growth rate, and crucible and bottom-heater temperatures are tested as processing parameters for satisfying the constrained thermal-capillary problem over a range of melt volumes corresponding to the sequence occuring during the batchwise Czochralski growth of a small-diameter silicon crystal. The applicability of each processing strategy is judged by the range of existence of the solution, in terms of melt volume and the values of the axial and radial temperature gradients in the crystal.

Design optimization of structural parameters for highly sensitive photonic crystal label-free biosensors.

Science.gov (United States)

Ju, Jonghyun; Han, Yun-ah; Kim, Seok-min

2013-03-07

The effects of structural design parameters on the performance of nano-replicated photonic crystal (PC) label-free biosensors were examined by the analysis of simulated reflection spectra of PC structures. The grating pitch, duty, scaled grating height and scaled TiO2 layer thickness were selected as the design factors to optimize the PC structure. The peak wavelength value (PWV), full width at half maximum of the peak, figure of merit for the bulk and surface sensitivities, and surface/bulk sensitivity ratio were also selected as the responses to optimize the PC label-free biosensor performance. A parametric study showed that the grating pitch was the dominant factor for PWV, and that it had low interaction effects with other scaled design factors. Therefore, we can isolate the effect of grating pitch using scaled design factors. For the design of PC-label free biosensor, one should consider that: (1) the PWV can be measured by the reflection peak measurement instruments, (2) the grating pitch and duty can be manufactured using conventional lithography systems, and (3) the optimum design is less sensitive to the grating height and TiO2 layer thickness variations in the fabrication process. In this paper, we suggested a design guide for highly sensitive PC biosensor in which one select the grating pitch and duty based on the limitations of the lithography and measurement system, and conduct a multi objective optimization of the grating height and TiO2 layer thickness for maximizing performance and minimizing the influence of parameter variation. Through multi-objective optimization of a PC structure with a fixed grating height of 550 nm and a duty of 50%, we obtained a surface FOM of 66.18 RIU-1 and an S/B ratio of 34.8%, with a grating height of 117 nm and TiO2 height of 210 nm.

Design Optimization of Structural Parameters for Highly Sensitive Photonic Crystal Label-Free Biosensors

Directory of Open Access Journals (Sweden)

Yun-ah Han

2013-03-01

Full Text Available The effects of structural design parameters on the performance of nano-replicated photonic crystal (PC label-free biosensors were examined by the analysis of simulated reflection spectra of PC structures. The grating pitch, duty, scaled grating height and scaled TiO2 layer thickness were selected as the design factors to optimize the PC structure. The peak wavelength value (PWV, full width at half maximum of the peak, figure of merit for the bulk and surface sensitivities, and surface/bulk sensitivity ratio were also selected as the responses to optimize the PC label-free biosensor performance. A parametric study showed that the grating pitch was the dominant factor for PWV, and that it had low interaction effects with other scaled design factors. Therefore, we can isolate the effect of grating pitch using scaled design factors. For the design of PC-label free biosensor, one should consider that: (1 the PWV can be measured by the reflection peak measurement instruments, (2 the grating pitch and duty can be manufactured using conventional lithography systems, and (3 the optimum design is less sensitive to the grating height and TiO2 layer thickness variations in the fabrication process. In this paper, we suggested a design guide for highly sensitive PC biosensor in which one select the grating pitch and duty based on the limitations of the lithography and measurement system, and conduct a multi objective optimization of the grating height and TiO2 layer thickness for maximizing performance and minimizing the influence of parameter variation. Through multi-objective optimization of a PC structure with a fixed grating height of 550 nm and a duty of 50%, we obtained a surface FOM of 66.18 RIU−1 and an S/B ratio of 34.8%, with a grating height of 117 nm and TiO2 height of 210 nm.

Purification, crystallization and preliminary crystallographic analysis of deoxyuridine triphosphate nucleotidohydrolase from Arabidopsis thaliana

Energy Technology Data Exchange (ETDEWEB)

Bajaj, Mamta [School of Biological Sciences, University of Nebraska-Lincoln, Manter Hall, Lincoln, Nebraska 68588-0304 (United States); Moriyama, Hideaki, E-mail: hmoriyama2@unl.edu [Department of Chemistry, e-Toxicology and Biotechnology, University of Nebraska-Lincoln, Hamilton Hall, Lincoln, Nebraska 68588-0304 (United States); School of Biological Sciences, University of Nebraska-Lincoln, Manter Hall, Lincoln, Nebraska 68588-0304 (United States)

2007-05-01

The first crystallization of deoxyuridine triphosphate nucleotidohydrolase from plant, Arabidopsis thaliana, has been performed. An additive, taurine, was effective in producing the single crystal. The deoxyuridine triphosphate nucleotidohydrolase gene from Arabidopsis thaliana was expressed and the gene product was purified. Crystallization was performed by the hanging-drop vapour-diffusion method at 298 K using 2 M ammonium sulfate as the precipitant. X-ray diffraction data were collected to 2.2 Å resolution using Cu Kα radiation. The crystal belongs to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 69.90, b = 70.86 Å, c = 75.55 Å. Assuming the presence of a trimer in the asymmetric unit, the solvent content was 30%, with a V{sub M} of 1.8 Å{sup 3} Da{sup −1}.

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

International Nuclear Information System (INIS)

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

2010-01-01

The invertase from X. dendrorhous has been purified, deglycosylated and crystallized and diffraction data have been collected to 2.3 Å resolution. 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

PDF analysis on re-crystallized structure from amorphous BiT

Energy Technology Data Exchange (ETDEWEB)

Yoneda, Yasuhiro [Japan Atomic Energy Research Institute, Synchrotron Radiation Research Center, Kouto 1-1-1, Mikazuki-cho, Sayo-gun, Hyogo 679-5148 (Japan)]. E-mail: yoneda@spring8.or.jp; Kohara, Shinji [Synchrotron Radiation Research Laboratory, Japan Synchrotron Radiation, Research Institute, Kouto 1-1-1, Mikazuki-cho, Sayo-gun, Hyogo 679-5198 (Japan); Hamazaki, Shin' ichi [Department of Electronics, Iwaki Meisei University, Iino 5-5-1, Chuohdai, Fukushima 970-8551 (Japan); Takashige, Masaaki [Department of Electronics, Iwaki Meisei University, Iino 5-5-1, Chuohdai, Fukushima 970-8551 (Japan); Mizuki, Jun' ichiro [Japan Atomic Energy Research Institute, Synchrotron Radiation Research Center, Kouto 1-1-1, Mikazuki-cho, Sayo-gun, Hyogo 679-5148 (Japan)

2005-08-15

A glass sample of composition Bi{sub 4}Ti{sub 3}O{sub 12} was prepared by rapid quenching. The as-quenched sample was confirmed to be amorphous by synchrotron X-ray measurements. The crystallization process of the amorphous sample was also investigated by high-energy X-ray diffraction and by atomic pair distribution function analysis. The perovskite layer in the crystal Bi{sub 4}Ti{sub 3}O{sub 12} is transformed to a pyrochlore structure in the amorphous sample. The amorphous sample first crystallized to a metastable phase by acquiring long-range ordering of the pyrochlore structure at T {sub cryst1}, and then secondary crystallized into a reverted Bi{sub 4}Ti{sub 3}O{sub 12} structure at T {sub cryst2}.

Experimental investigation and crystal-field modeling of Er{sup 3+} energy levels in GSGG crystal

Energy Technology Data Exchange (ETDEWEB)

Gao, J.Y., E-mail: jygao1985@sina.com [Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Hefei 230031 (China); Sun, D.L.; Zhang, Q.L. [Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Hefei 230031 (China); Wang, X.F. [Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Hefei 230031 (China); Graduate School of the Chinese Academy of Sciences, Beijing 100049 (China); Liu, W.P.; Luo, J.Q.; Sun, G.H.; Yin, S.T. [Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Hefei 230031 (China)

2016-06-25

The Er{sup 3+}-doped Gd{sub 3}Sc{sub 2}Ga{sub 3}O{sub 12} (Er{sup 3+}:GSGG) single crystal, a excellent medium of the mid-infrared and anti-radiation solid state laser pumped by laser diode, was grown by Czochralski method successfully. The absorption spectra were measured and analyzed in a wider spectral wavelength range of 350–1700 nm at different temperatures of 7.6, 77, 200 and 300 K. The free-ions and crystal-field parameters were fitted to the experimental energy levels with the root mean square deviation of 9.86 cm{sup −1}. According to the crystal-field calculations, 124 degenerate energy levels of Er{sup 3+} in GSGG host crystals were assigned. The fitting results of free-ions and crystal-field parameters were compared with those already reported of Er{sup 3+}:YSGG. The results indicated that the free-ions parameters for Er{sup 3+} in GSGG host are similar to those in YSGG host crystals, and the crystal-field interaction of GSGG is weaker than that of YSGG, which may result in the better laser characterization of Er{sup 3+}:GSGG crystal. - Highlights: • The efficient diode-end-pumped laser crystal Er:GSGG has been grown successfully. • The absorption spectra of Er:GSGG have been measured in range of 350–1700 nm. • The fitting result is very well for the root mean square deviation is 9.86 cm{sup −1}. • The 124 levels of Er:GSGG have been assigned from the crystal-field calculations.

Study on sensing property of one-dimensional ring mirror-defect photonic crystal

Science.gov (United States)

Chen, Ying; Luo, Pei; Cao, Huiying; Zhao, Zhiyong; Zhu, Qiguang

2018-02-01

Based on the photon localization and the photonic bandgap characteristics of photonic crystals (PCs), one-dimensional (1D) ring mirror-defect photonic crystal structure is proposed. Due to the introduction of mirror structure, a defect cavity is formed in the center of the photonic crystal, and then the resonant transmission peak can be obtained in the bandgap of transmission spectrum. The transfer matrix method is used to establish the relationship model between the resonant transmission peak and the structure parameters of the photonic crystals. Using the rectangular air gate photonic crystal structure, the dynamic monitoring of the detected gas sample parameters can be achieved from the shift of the resonant transmission peak. The simulation results show that the Q-value can attain to 1739.48 and the sensitivity can attain to 1642 nm ṡ RIU-1, which demonstrates the effectiveness of the sensing structure. The structure can provide certain theoretical reference for air pollution monitoring and gas component analysis.

Expression, purification, crystallization and preliminary X-ray analysis of wild-type and of an active-site mutant of glyceraldehyde-3-phosphate dehydrogenase from Campylobacter jejuni

International Nuclear Information System (INIS)

Tourigny, David S.; Elliott, Paul R.; Edgell, Louise J.; Hudson, Gregg M.; Moody, Peter C. E.

2010-01-01

The cloning, expression, purification, crystallization and preliminary X-ray analysis of wild-type and of an active-site mutant of C. jejuni glyceraldehyde-3-phosphate dehydrogenase is reported. The genome of the enteric pathogen Campylobacter jejuni encodes a single glyceraldehyde-3-phosphate dehydrogenase that can utilize either NADP + or NAD + as coenzymes for the oxidative phosphorylation of glyceraldehyde-3-phosphate to 1,3-diphosphoglycerate. Here, the cloning, expression, purification, crystallization and preliminary X-ray analysis of both the wild type and an active-site mutant of the enzyme are presented. Preliminary X-ray analysis revealed that in both cases the crystals diffracted to beyond 1.9 Å resolution. The space group is shown to be I4 1 22, with unit-cell parameters a = 90.75, b = 90.75, c = 225.48 Å, α = 90.46, β = 90.46, γ = 222.79°; each asymmetric unit contains only one subunit of the tetrameric enzyme

Parallelization for X-ray crystal structural analysis program

Energy Technology Data Exchange (ETDEWEB)

Watanabe, Hiroshi [Japan Atomic Energy Research Inst., Tokyo (Japan); Minami, Masayuki; Yamamoto, Akiji

1997-10-01

In this report we study vectorization and parallelization for X-ray crystal structural analysis program. The target machine is NEC SX-4 which is a distributed/shared memory type vector parallel supercomputer. X-ray crystal structural analysis is surveyed, and a new multi-dimensional discrete Fourier transform method is proposed. The new method is designed to have a very long vector length, so that it enables to obtain the 12.0 times higher performance result that the original code. Besides the above-mentioned vectorization, the parallelization by micro-task functions on SX-4 reaches 13.7 times acceleration in the part of multi-dimensional discrete Fourier transform with 14 CPUs, and 3.0 times acceleration in the whole program. Totally 35.9 times acceleration to the original 1CPU scalar version is achieved with vectorization and parallelization on SX-4. (author)

Preliminary X-ray analysis of twinned crystals of sarcosine dimethylglycine methyltransferase from Halorhodospira halochoris

International Nuclear Information System (INIS)

Kallio, Juha Pekka; Jänis, Janne; Nyyssölä, Antti; Hakulinen, Nina; Rouvinen, Juha

2009-01-01

The crystallization and preliminary X-ray diffraction analysis of sarcosine dimethylglycine methyltransferase from H. halochoris is reported. Sarcosine dimethylglycine methyltransferase (EC 2.1.1.157) is an enzyme from the extremely halophilic anaerobic bacterium Halorhodospira halochoris. This enzyme catalyzes the twofold methylation of sarcosine to betaine, with S-adenosylmethionine (AdoMet) as the methyl-group donor. This study presents the crystallization and preliminary X-ray analysis of recombinant sarcosine dimethylglycine methyltransferase produced in Escherichia coli. Mass spectroscopy was used to determine the purity and homogeneity of the enzyme material. Two different crystal forms, which initially appeared to be hexagonal and tetragonal, were obtained. However, on analyzing the diffraction data it was discovered that both crystal forms were pseudo-merohedrally twinned. The true crystal systems were monoclinic and orthorhombic. The monoclinic crystal diffracted to a maximum of 2.15 Å resolution and the orthorhombic crystal diffracted to 1.8 Å resolution

Expression, purification, crystallization and preliminary crystallographic analysis of SpaA, a major pilin from Corynebacterium diphtheriae

International Nuclear Information System (INIS)

Kang, Hae Joo; Paterson, Neil G.; Baker, Edward N.

2009-01-01

SpaA, one of the major pilins of C. diphtheriae, has been expressed, purified and crystallized and X-ray diffraction data have been collected to 1.6 Å resolution. Bacterial pili are cell-surface organelles that are critically involved in adhesion to host cells, leading to the colonization of host tissues and the establishment of infections. Whereas the pili of Gram-negative bacteria have been extensively studied, those of Gram-positive bacteria came to light only recently after the discovery and characterization of Corynebacterium diphtheriae pili. These newly discovered pili are formed by the covalent polymerization of pilin subunits catalyzed by sortase enzymes, making them fundamentally different from the noncovalent pilin assemblies of Gram-negative bacteria. Here, the expression, crystallization and preliminary crystallographic analysis of SpaA, which forms the shaft of one of the three types of pili expressed by C. diphtheriae, are reported. SpaA 53–486 crystals diffracted to 1.6 Å resolution and belonged to space group P2 1 2 1 2 1 , with unit-cell parameters a = 34.9, b = 64.1, c = 198.7 Å, α = β = γ = 90°

Expression, purification, crystallization and preliminary X-ray analysis of the d-alanyl carrier protein DltC from Staphylococcus epidermidis

International Nuclear Information System (INIS)

Huang, Chi-Hung; Kao, Chao-Hung; Yang, Chia-Shin; Chang, Chi-Huang; Chen, Sheng-Chia; Kuan, Shu-Min; Su, Yen-Chao; Huang, Yu-Han; Chang, Ming-Chung; Chen, Yeh

2012-01-01

The S. epidermidis carrier protein DltC has been crystallized in order to elucidate the functional role of DltC in the alanylation of lipoteichoic acids in bacteria. The d-alanyl lipoteichoic acids (d-alanyl LTAs) present in the cell walls of Gram-positive bacteria play crucial roles in autolysis, cation homeostasis and biofilm formation. The alanylation of LTAs requires the d-alanyl carrier protein DltC to transfer d-Ala onto a membrane-associated LTA. Here, DltC from Staphylococcus epidermidis (SeDltC) was purified and crystallized using the sitting-drop vapour-diffusion method. The crystals diffracted to a resolution of 1.83 Å and belonged to space group P2, with unit-cell parameters a = 66.26, b = 53.28, c = 88.05 Å, β = 98.22°. The results give a preliminary crystallographic analysis of SeDltC and shed light on the functional role of DltC in the alanylation of LTAs

Cloning, overexpression, crystallization and preliminary X-ray crystallographic analysis of a slow-processing mutant of penicillin G acylase from Kluyvera citrophila

International Nuclear Information System (INIS)

Varshney, Nishant Kumar; Ramasamy, Sureshkumar; Brannigan, James A.; Wilkinson, Anthony J.; Suresh, C. G.

2013-01-01

The pac gene encoding penicillin G acylase from K. citrophila was cloned and a slow-processing site-directed mutant was prepared, expressed, purified and crystallized. Triclinic and monoclinic crystal forms were obtained which diffracted to 2.5 and 3.5 Å resolution, respectively. Kluyvera citrophila penicillin G acylase (KcPGA) has recently attracted increased attention relative to the well studied and commonly used Escherichia coli PGA (EcPGA) because KcPGA is more resilient to harsh conditions and is easier to immobilize for the industrial hydrolysis of natural penicillins to generate the 6-aminopenicillin (6-APA) nucleus, which is the starting material for semi-synthetic antibiotic production. Like other penicillin acylases, KcPGA is synthesized as a single-chain inactive pro-PGA, which upon autocatalytic processing becomes an active heterodimer of α and β chains. Here, the cloning of the pac gene encoding KcPGA and the preparation of a slow-processing mutant precursor are reported. The purification, crystallization and preliminary X-ray analysis of crystals of this precursor protein are described. The protein crystallized in two different space groups, P1, with unit-cell parameters a = 54.0, b = 124.6, c = 135.1 Å, α = 104.1, β = 101.4, γ = 96.5°, and C2, with unit-cell parameters a = 265.1, b = 54.0, c = 249.2 Å, β = 104.4°, using the sitting-drop vapour-diffusion method. Diffraction data were collected at 100 K and the phases were determined using the molecular-replacement method. The initial maps revealed electron density for the spacer peptide

Novel variational approach for analysis of photonic crystal slabs

International Nuclear Information System (INIS)

Aram, Mohammad Hasan; Khorasani, Sina

2015-01-01

We propose a new method, based on variational principle, for the analysis of photonic crystal (PC) slabs. Most of the methods used today treat PC slabs as three-dimensional (3D) crystal, and this makes these methods very time and/or memory consuming. In our proposed method, we use the Bloch theorem to expand the field on infinite plane waves, whose amplitudes depend on the component perpendicular to the slab surface. By approximating these amplitudes with appropriate functions, we can find modes of PC slabs almost as fast as we can find modes of two-dimensional crystals. In addition to this advantage, we can also calculate radiation modes with this method, which is not feasible with the 3D plane wave expansion method. (paper)

Crystallization and preliminary X-ray analysis of the receiver domain of a putative response regulator, BPSL0128, from Burkholderia pseudomallei

International Nuclear Information System (INIS)

Abd Aziz, Abd Ghani; Sedelnikova, Svetlana E.; Ruzheinikov, Sergey N.; Thorpe, Simon; Mohamed, Rahmah; Nathan, Sheila; Rafferty, John B.; Baker, Patrick J.; Rice, David W.

2012-01-01

The receiver domain of a putative response regulator from B. pseudomallei, BPSL0128, has been crystallized in a form suitable for X-ray analysis. bpsl0128, a gene encoding a putative response regulator from Burkholderia pseudomallei strain D286, has been cloned into a pETBLUE-1 vector system, overexpressed in Escherichia coli and purified. The full-length protein is degraded during purification to leave a fragment corresponding to the putative receiver domain, and crystals of this protein that diffracted to beyond 1.75 Å resolution have been grown by the hanging-drop vapour-diffusion technique using PEG 6000 as the precipitant. The crystals belonged to one of the enantiomorphic pair of space groups P3 1 21 and P3 2 21, with unit-cell parameters a = b = 65.69, c = 105.01 Å and either one or two molecules in the asymmetric unit

Crystallization and preliminary X-ray analysis of native and selenomethionyl vinorine synthase from Rauvolfia serpentina.

Science.gov (United States)

Ma, Xueyan; Koepke, Juergen; Bayer, Anja; Fritzsch, Günter; Michel, Hartmut; Stöckigt, Joachim

2005-06-01

Vinorine synthase (VS) is a central enzyme of the biosynthesis of the antiarrhythmic drug ajmaline and is a member of the BAHD superfamily of acyltransferases. So far, no three-dimensional structure with significant sequence homology with VS is known. Crystals of VS and selenomethionyl-labelled VS from the medicinal plant Rauvolfia serpentina have been obtained by the hanging-drop technique at 305 K with ammonium sulfate and PEG 400 as precipitants. VS crystals diffract to 2.8 A and belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 82.3, b = 89.6, c = 136.2 A. The selenomethionyl VS crystal was nearly isomorphous with the VS crystal.

Ectodomain of plasmodesmata-localized protein 5 in Arabidopsis: expression, purification, crystallization and crystallographic analysis.

Science.gov (United States)

Wang, Xiaocui; Zhu, Peiyan; Qu, Shanshan; Zhao, Jie; Singh, Prashant K; Wang, Wei

2017-09-01

Plasmodesmata-localized protein 5 (PDLP5) is a cysteine-rich receptor-like protein which is localized on the plasmodesmata of Arabidopsis thaliana. Overexpression of PDLP5 can reduce the permeability of the plasmodesmata and further affect the cell-to-cell movement of viruses and macromolecules in plants. The ectodomain of PDLP5 contains two DUF26 domains; however, the function of these domains is still unknown. Here, the ectodomain of PDLP5 from Arabidopsis was cloned and overexpressed using an insect expression system and was then purified and crystallized. X-ray diffraction data were collected to 1.90 Å resolution and were indexed in space group P1, with unit-cell parameters a = 41.9, b = 48.1, c = 62.2 Å, α = 97.3, β = 103.1, γ = 99.7°. Analysis of the crystal content indicated that there are two molecules in the asymmetric unit, with a Matthews coefficient of 2.51 Å 3  Da -1 and a solvent content of 50.97%.

Dislocations and point defects in hydrostatically compressed crystal

International Nuclear Information System (INIS)

Kosevich, A.M.; Tokij, V.V.; Strel'tsov, V.A.

1978-01-01

Within the framework of the theory of finite deformations, the elastic fields are considered, which are induced by the sources of internal stresses in a crystal compressed under a high pressure. In the case of a hydrostatically compressed crystal with defects, the use of a variation principle is discussed. Using the smallness of distorsions, the linear theory of elastic fields of defects in the crystal compressed under a high pressure, is developed. An analysis of the main relationships of the theory results in the following conclusion: in a course of the linear approximation the taking into account of the hydrostatic pressure brings to the renorming of the elasticity moduli and to the replacing of the hydrostatic parameters of defects by their values in the compressed crystal. That conclusion allows the results of the elasticity linear theory of the crystal with defects to be used to the full extent

Cogeneration: Key feasibility analysis parameters

International Nuclear Information System (INIS)

Coslovi, S.; Zulian, A.

1992-01-01

This paper first reviews the essential requirements, in terms of scope, objectives and methods, of technical/economic feasibility analyses applied to cogeneration systems proposed for industrial plants in Italy. Attention is given to the influence on overall feasibility of the following factors: electric power and fuel costs, equipment coefficients of performance, operating schedules, maintenance costs, Italian Government taxes and financial and legal incentives. Through an examination of several feasibility studies that were done on cogeneration proposals relative to different industrial sectors, a sensitivity analysis is performed on the effects of varying the weights of different cost benefit analysis parameters. With the use of statistical analyses, standard deviations are then determined for key analysis parameters, and guidelines are suggested for analysis simplifications

Purification, crystallization and preliminary X-ray analysis of urease from pigeon pea (Cajanus cajan)

Energy Technology Data Exchange (ETDEWEB)

Balasubramanian, Anuradha; Ponnuraj, Karthe, E-mail: pkarthe@hotmail.com [Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025 (India)

2008-07-01

Urease from pigeon pea was purified and crystallized and X-ray diffraction data were collected at 2.5 Å resolution. Urease is a seed protein that is common to most Leguminosae. It also occurs in many bacteria, fungi and several species of yeast. Urease catalyzes the hydrolysis of urea to ammonia and carbon dioxide, thus allowing organisms to use exogenous and internally generated urea as a nitrogen source. Urease from pigeon pea seeds has been purified to electrophoretic homogeneity using a series of steps involving ammonium sulfate fractionation, acid precipitation, ion-exchange and size-exclusion chromatography techniques. The pigeon pea urease was crystallized and the resulting crystals diffracted to 2.5 Å resolution. The crystals belong to the rhombohedral space group R32, with unit-cell parameters a = b = 176.29, c = 346.44 Å.

Purification, crystallization and preliminary X-ray analysis of urease from pigeon pea (Cajanus cajan)

International Nuclear Information System (INIS)

Balasubramanian, Anuradha; Ponnuraj, Karthe

2008-01-01

Urease from pigeon pea was purified and crystallized and X-ray diffraction data were collected at 2.5 Å resolution. Urease is a seed protein that is common to most Leguminosae. It also occurs in many bacteria, fungi and several species of yeast. Urease catalyzes the hydrolysis of urea to ammonia and carbon dioxide, thus allowing organisms to use exogenous and internally generated urea as a nitrogen source. Urease from pigeon pea seeds has been purified to electrophoretic homogeneity using a series of steps involving ammonium sulfate fractionation, acid precipitation, ion-exchange and size-exclusion chromatography techniques. The pigeon pea urease was crystallized and the resulting crystals diffracted to 2.5 Å resolution. The crystals belong to the rhombohedral space group R32, with unit-cell parameters a = b = 176.29, c = 346.44 Å

Expression, purification, crystallization and preliminary crystallographic analysis of MxiH, a subunit of the Shigella flexneri type III secretion system needle

Energy Technology Data Exchange (ETDEWEB)

Deane, Janet E.; Cordes, Frank S.; Roversi, Pietro [Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford (United Kingdom); Johnson, Steven [Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford (United Kingdom); Sir William Dunn School of Pathology, University of Oxford (United Kingdom); Kenjale, Roma; Picking, William D.; Picking, Wendy L. [Department of Molecular Biosciences, University of Kansas (United States); Lea, Susan M., E-mail: susan.lea@biop.ox.ac.uk [Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford (United Kingdom); Sir William Dunn School of Pathology, University of Oxford (United Kingdom); Blocker, Ariel [Sir William Dunn School of Pathology, University of Oxford (United Kingdom); Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford (United Kingdom)

2006-03-01

A monodisperse truncation mutant of MxiH, the subunit of the S. flexneri type III secretion system needle, has been crystallized. SeMet derivatives and a uranyl derivative have undergone preliminary crystallographic analysis. A monodisperse truncation mutant of MxiH, the subunit of the needle from the Shigella flexneri type III secretion system (TTSS), has been overexpressed and purified. Crystals were grown of native and selenomethionine-labelled MxiH{sub CΔ5} and diffraction data were collected to 1.9 Å resolution. The crystals belong to space group C2, with unit-cell parameters a = 183.4, b = 28.1, c = 27.8 Å, β = 96.5°. An anomalous difference Patterson map calculated with the data from the SeMet-labelled crystals revealed a single peak on the Harker section v = 0. Inspection of a uranyl derivative also revealed one peak in the isomorphous difference Patterson map on the Harker section v = 0. Analysis of the self-rotation function indicates the presence of a twofold non-crystallographic symmetry axis approximately along a. The calculated Matthews coefficient is 1.9 Å{sup 3} Da{sup −1} for two molecules per asymmetric unit, corresponding to a solvent content of 33%.

Purification, crystallization and preliminary crystallographic analysis of biotin protein ligase from Staphylococcus aureus

International Nuclear Information System (INIS)

Pendini, Nicole R.; Polyak, Steve W.; Booker, Grant W.; Wallace, John C.; Wilce, Matthew C. J.

2008-01-01

The biotin protein ligase from S. aureus has been overexpressed in E. coli, purified, crystallized by the hanging-drop vapour-diffusion method and analysed using X-ray diffraction. Biotin protein ligase from Staphylococcus aureus catalyses the biotinylation of acetyl-CoA carboxylase and pyruvate carboxylase. Recombinant biotin protein ligase from S. aureus has been cloned, expressed and purified. Crystals were grown using the hanging-drop vapour-diffusion method using PEG 8000 as the precipitant at 295 K. X-ray diffraction data were collected to 2.3 Å resolution from crystals using synchrotron X-ray radiation at 100 K. The diffraction was consistent with the tetragonal space group P4 2 2 1 2, with unit-cell parameters a = b = 93.665, c = 131.95

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

Energy Technology Data Exchange (ETDEWEB)

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

2010-05-01

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

Mapping residual stresses in PbWO4 crystals using photo-elastic analysis

International Nuclear Information System (INIS)

Lebeau, M.; Gobbi, L.; Majni, G.; Paone, N.; Pietroni, P.; Rinaldi, D.

2005-01-01

Large scintillating crystals are affected by internal stresses induced by the crystal growth temperature gradient remanence. Cutting boules (ingots) into finished crystal shapes allows for a partial tension relaxation but residual stresses remain the main cause of breaking. Quality control of residual stresses is essential in the application of Scintillating Crystals to high-energy physics calorimeters (e.g. CMS ECAL at CERN LHC). In this context the industrial process optimisation towards stress reduction is mandatory. We propose a fast technique for testing samples during the production process in order to evaluate the residual stress distribution after the first phases of mechanical processing. We mapped the stress distribution in PbWO 4 slabs cut from the same production boule. The analysis technique is based on the stress intensity determination using the photo-elastic properties of the samples. The stress distribution is mapped in each sample. The analysis shows that there are regions of high residual tension close to the seed position and at the boule periphery. These results should allow for adapting the industrial process to producing crystals with lower residual stresses

Crystal-field effect in UO2

International Nuclear Information System (INIS)

Gajek, Z.; Lahalle, M.P.; Krupa, J.C.; Mulak, J.

1988-01-01

Simple ab initio model perturbation calculations of the crystal-field parameters for the U 4+ ion in UO 2 crystals are reported. The crystal-field parameters obtained, B 0 4 = -7130 cm -1 and B 0 6 = 2890 cm -1 , turn out to be much lower in value, particularly the first one, than those usually assumed for this compound. They are found, however, to agree with new spectroscopic data and recent inelastic neutron scattering measurements. (orig.)

Purification, crystallization and preliminary crystallographic analysis of Arabidopsis thaliana imidazoleglycerol-phosphate dehydratase

International Nuclear Information System (INIS)

Glynn, Steven E.; Baker, Patrick J.; Sedelnikova, Svetlana E.; Levy, Colin W.; Rodgers, H. Fiona; Blank, Jutta; Hawkes, Timothy R.; Rice, David W.

2005-01-01

Imidazoleglycerol-phosphate dehydratase from A. thaliana has been overexpressed, purified and crystallized and data have been collected to 3 Å resolution. Imidazoleglycerol-phosphate dehydratase catalyses the sixth step of the histidine-biosynthesis pathway in plants and microorganisms and has been identified as a possible target for the development of novel herbicides. Arabidopsis thaliana IGPD has been cloned and overexpressed in Escherichia coli, purified and subsequently crystallized in the presence of manganese. Under these conditions, the inactive trimeric form of the metal-free enzyme is assembled into a fully active species consisting of a 24-mer exhibiting 432 symmetry. X-ray diffraction data have been collected to 3.0 Å resolution from a single crystal at 293 K. The crystal belongs to space group R3, with approximate unit-cell parameters a = b = 157.9, c = 480.0 Å, α = β = 90, γ = 120° and with either 16 or 24 subunits in the asymmetric unit. A full structure determination is under way in order to provide insights into the mode of subunit assembly and to initiate a programme of rational herbicide design

The influence of high hydrostatic pressure on lattice parameters of a single crystal of BaTiO3

International Nuclear Information System (INIS)

Malinowski, M.; Lukaszewicz, K.; Asbrink, S.

1986-01-01

The lattice parameters of a single crystal of BaTiO 3 have been measured under high hydrostatic pressure up to 5 GPa using a diamond-anvil high-pressure cell of a new design. The lattice becomes cubic at 2.08(8) GPa and stays cubic at higher pressures. The pressure dependence of the tetragonal-cubic transition temperature is estimated to be -46 K GPa -1 . (orig.)

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

Energy Technology Data Exchange (ETDEWEB)

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

2008-05-01

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

Crystal growth, spectral properties, and laser demonstration of laser crystal Nd:LYSO

Science.gov (United States)

Li, D. Z.; Xu, X. D.; Zhou, D. H.; Zhuang, S. D.; Wang, Z. P.; Xia, C. T.; Wu, F.; Xu, J.

2010-11-01

A Nd:LYSO crystal has been grown by the Czochralski technique. The cell parameters were analyzed with X-ray diffraction (XRD). The Judd-Ofelt intense parameters Ω2,4,6 were obtained to be 2.65, 5.75, and 7.37×10-20 cm2, respectively. The absorption and emission cross sections and the branching ratios were calculated. The large absorption cross section (6.14×10-20 cm2) and broad absorption band (5 nm) around 811 nm indicate that this crystal can be pumped efficiently by laser diodes. The broad emission band from the 4F3/2 multiplet shows that the crystal is a promising medium for ultrashort pulse lasers. Pumped by a laser diode, the maximum 814 mW continuous-wave laser output has been obtained with a slope efficiency of 28.9%. All the results show that this crystal is a promising laser material.

Crystal growth, spectral properties, and laser demonstration of laser crystal Nd:LYSO

International Nuclear Information System (INIS)

Li, D Z; Xu, X D; Zhou, D H; Xia, C T; Wu, F; Zhuang, S D; Wang, Z P; Xu, J

2010-01-01

A Nd:LYSO crystal has been grown by the Czochralski technique. The cell parameters were analyzed with X-ray diffraction (XRD). The Judd-Ofelt intense parameters Ω 2,4,6 were obtained to be 2.65, 5.75, and 7.37×10 -20 cm 2 , respectively. The absorption and emission cross sections and the branching ratios were calculated. The large absorption cross section (6.14×10 -20 cm 2 ) and broad absorption band (5 nm) around 811 nm indicate that this crystal can be pumped efficiently by laser diodes. The broad emission band from the 4 F 3/2 multiplet shows that the crystal is a promising medium for ultrashort pulse lasers. Pumped by a laser diode, the maximum 814 mW continuous-wave laser output has been obtained with a slope efficiency of 28.9%. All the results show that this crystal is a promising laser material

Crystallization and preliminary diffraction analysis of Wzi, a member of the capsule export and assembly pathway in Escherichia coli

International Nuclear Information System (INIS)

Bushell, Simon R.; Lou, Hubing; Wallat, Gregor D.; Beis, Konstantinos; Whitfield, Chris; Naismith, James H.

2010-01-01

Wzi is a membrane protein from E. coli thought to be involved in the attachment of capsular polysaccharides to the bacterial surface. This reports describes recombinant Wzi’s purification, crystallization and the results of initial diffraction studies. External polysaccharide capsules provide a physical barrier that is employed by many species of bacteria for the purposes of host evasion and persistence. Wzi is a 53 kDa outer membrane β-barrel protein that is thought to play a role in the attachment of group 1 capsular polysaccharides to the cell surface. The purification and crystallization of an Escherichia coli homologue of Wzi is reported and diffraction data from native and selenomethionine-incorporated protein crystals are presented. Crystals of C-terminally His 6 -tagged Wzi diffracted to 2.8 Å resolution. Data processing showed that the crystals belonged to the orthorhombic space group C222, with unit-cell parameters a = 128.8, b = 152.8, c = 94.4 Å, α = β = γ = 90°. A His-tagged selenomethionine-containing variant of Wzi has also been crystallized in the same space group and diffraction data have been recorded to 3.8 Å resolution. Data processing shows that the variant crystal has similar unit-cell parameters to the native crystal

Synthesis and single crystal X-ray analysis of two griseofulvin metabolites

DEFF Research Database (Denmark)

Rønnest, Mads Holger; Harris, Pernille; Gotfredsen, Charlotte Held

2010-01-01

The two phenols, 6-O-desmethyl griseofulvin and 4-O-desmethyl griseofulvin are metabolites of the antifungal drug griseofulvin. Herein, we present an improved synthesis of the 6-phenol derivative, and an unequivocal proof of both structures by single-crystal X-ray analysis.......The two phenols, 6-O-desmethyl griseofulvin and 4-O-desmethyl griseofulvin are metabolites of the antifungal drug griseofulvin. Herein, we present an improved synthesis of the 6-phenol derivative, and an unequivocal proof of both structures by single-crystal X-ray analysis....

Crystal Growth of Ca3Nb(Ga1−xAlx3Si2O14 Piezoelectric Single Crystals with Various Al Concentrations

Directory of Open Access Journals (Sweden)

Yuui Yokota

2015-08-01

Full Text Available Ca3Nb(Ga1−xAlx3Si2O14 (CNGAS single crystals with various Al concentrations were grown by a micro-pulling-down (µ-PD method and their crystal structures, chemical compositions, crystallinities were investigated. CNGAS crystals with x = 0.2, 0.4 and 0.6 indicated a single phase of langasite-type structure without any secondary phases. In contrast, the crystals with x = 0.8 and 1 included some secondary phases in addition to the langasite-type phase. Lattice parameters, a- and c-axes lengths, of the langasite-type phase systematically decreased with an increase of Al concentration. The results of chemical composition analysis revealed that the actual Al concentrations in as-grown crystals were almost consistent with the nominal compositions. In addition, there was no large segregation of each cation along the growth direction.

Crystallization and preliminary X-ray analysis of the chemokine-binding protein from orf virus (Poxviridae)

International Nuclear Information System (INIS)

Couñago, Rafael Miguez; Fleming, Stephen B.; Mercer, Andrew A.; Krause, Kurt L.

2010-01-01

The chemokine-binding protein from orf virus was purified and crystallized. The morphology and diffraction behaviour of these crystals was significantly improved through the use of additives known as Silver Bullets. The parapoxvirus orf virus (ORFV) encodes a chemokine-binding protein (CBP) that functions to downregulate the host’s immune response at the site of infection by blocking the chemokine-induced recruitment of immune cells. In order to shed light on the structural determinants of CBP–chemokine binding, ORFV CBP was crystallized as part of an ongoing structure–function study on this protein. ORFV CBP crystals were obtained by the sitting-drop vapour-diffusion technique using ammonium citrate as a precipitant. The crystal quality was greatly improved through the addition of small-molecule additives to the crystallization mother liquor. ORFV CBP crystals diffracted X-rays to 2.50 Å resolution and belonged to the hexagonal space group P6 1 22 or its enantiomorph P6 5 22, with unit-cell parameters a = b = 75.62, c = 282.49 Å, α = 90, β = 90, γ = 120°

Uncertainty, Sensitivity Analysis, and Causal Identification in the Arctic using a Perturbed Parameter Ensemble of the HiLAT Climate Model

Energy Technology Data Exchange (ETDEWEB)

Hunke, Elizabeth Clare [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Urrego Blanco, Jorge Rolando [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Urban, Nathan Mark [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2018-02-12

Coupled climate models have a large number of input parameters that can affect output uncertainty. We conducted a sensitivity analysis of sea ice proper:es and Arc:c related climate variables to 5 parameters in the HiLAT climate model: air-ocean turbulent exchange parameter (C), conversion of water vapor to clouds (cldfrc_rhminl) and of ice crystals to snow (micro_mg_dcs), snow thermal conduc:vity (ksno), and maximum snow grain size (rsnw_mlt). We used an elementary effect (EE) approach to rank their importance for output uncertainty. EE is an extension of one-at-a-time sensitivity analyses, but it is more efficient in sampling multi-dimensional parameter spaces. We looked for emerging relationships among climate variables across the model ensemble, and used causal discovery algorithms to establish potential pathways for those relationships.

Purification, crystallization and preliminary X-ray analysis of Enterococcus faecium aminoglycoside-2′′-phosphotransferase-Ib [APH(2′′)-Ib

International Nuclear Information System (INIS)

Walanj, Rupa; Young, Paul; Baker, Heather M.; Baker, Edward N.; Metcalf, Peter; Chow, Joseph W.; Lerner, Stephen; Vakulenko, Sergei; Smith, Clyde A.

2005-01-01

APH(2′′)-Ib is an enzyme responsible for high-level gentamicin resistance in E. faecium isolates. Native crystals of this enzyme have been prepared and preliminary X-ray diffraction experiments have been undertaken. Bacterial resistance to the aminoglycoside antibiotics is primarily the result of deactivation of the drugs. Three families of enzymes are responsible for this activity, with one such family being the aminoglycoside phosphotransferases (APHs). The gene encoding one of these enzymes, APH(2′′)-Ib, has been cloned and the protein (comprising 299 amino-acid residues) expressed in Escherichia coli, purified and crystallized in the presence of 16%(w/v) PEG 3350 and gentamicin. The crystals belong to the monoclinic space group P2 1 , with approximate unit-cell parameters a = 79.7, b = 58.8, c = 81.4 Å, β = 98.4°, and preliminary X-ray diffraction analysis is consistent with the presence of two molecules in the asymmetric unit. Synchrotron diffraction data to approximately 2.65 Å resolution were collected from a native APH(2′′)-Ib crystal at beamline BL9-2 at SSRL (Stanford, CA, USA). Selenium-substituted crystals have also been produced and structure determination is proceeding

Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of succinyl-diaminopimelate desuccinylase (Rv1202, DapE) from Mycobacterium tuberculosis

International Nuclear Information System (INIS)

Reinhard, Linda; Mueller-Dieckmann, Jochen; Weiss, Manfred S.

2012-01-01

M. tuberculosis succinyl-diaminopimelate desuccinylase, the enzyme which catalyzes the seventh step of the lysine-biosynthesis pathway, has been cloned, expressed, purified and crystallized. Preliminary X-ray diffraction analysis indicated the presence of pseudo-merohedral twinning in space group P2 1 , resulting in possible emulation of space group C222 1 . Succinyl-diaminopimelate desuccinylase from Mycobacterium tuberculosis (DapE, Rv1202) has been cloned, heterologously expressed in Escherichia coli and purified using standard chromatographic techniques. Diffraction-quality crystals were obtained at acidic pH from ammonium sulfate and PEG and diffraction data were collected from two crystals to resolutions of 2.40 and 2.58 Å, respectively. The crystals belonged to the monoclinic space group P2 1 , with unit-cell parameters a = 79.7, b = 76.0, c = 82.9 Å, β = 119°. The most probable content of the asymmetric unit was two molecules of DapE, which would correspond to a solvent content of 56%. Both examined crystals turned out to be pseudo-merohedrally twinned, with twin operator −h, −k, h + l and twin fractions of approximately 0.46 and 0.16, respectively

Expression, purification, crystallization and preliminary X-ray analysis of the human NORE1 SARAH domain

International Nuclear Information System (INIS)

Kim, Hye Jin; Hwang, Eunha; Han, Young-Hyun; Choi, Saehae; Lee, Woo Cheol; Kim, Hye-Yeon; Jeon, Young Ho; Cheong, Chaejoon; Cheong, Hae-Kap

2012-01-01

The crystallization of the human NORE1 SARAH domain is reported. NORE1 is an important tumour suppressor in human cancers that interacts with the pro-apoptotic protein kinase MST1/2 through SARAH domains. The SARAH domain (residues 366–413) of human NORE1 was expressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. The crystal diffracted to 2.7 Å resolution and belonged to space group P6 1 22, with unit-cell parameters a = b = 73.041, c = 66.092 Å, α = β = 90, γ = 120°

A single point mutation changes the crystallization behavior of Mycoplasma arthritidis-derived mitogen

Energy Technology Data Exchange (ETDEWEB)

Guo, Yi; Li, Zhong; Van Vranken, Sandra J. [Wadsworth Center, New York State Department of Health, Empire State Plaza, PO Box 509, Albany, New York 12201-0509 (United States); Li, Hongmin, E-mail: lih@wadsworth.org [Wadsworth Center, New York State Department of Health, Empire State Plaza, PO Box 509, Albany, New York 12201-0509 (United States); Department of Biomedical Sciences, School of Public Health, University at Albany, State University of New York, Empire State Plaza, PO Box 509, Albany, New York 12201-0509 (United States)

2006-03-01

The mutagenesis, crystallization and preliminary crystallographic analysis of M. arthritidis-derived mitogen is described. Mycoplasma arthritidis-derived mitogen (MAM) functions as a conventional superantigen (SAg). Although recombinant MAM has been crystallized by the hanging-drop vapour-diffusion method, the crystals diffracted poorly to only 5.0 Å resolution, with large unit-cell parameters a = 163.8, b = 93.0, c = 210.9 Å, β = 93.7° in the monoclinic space group P2{sub 1}. Unit-cell content analysis revealed that as many as 24 molecules could be present in the asymmetric unit. Systematic alanine mutagenesis was applied in order to search for mutants that give crystals of better quality. Two mutants, L50A and K201A, were crystallized under the same conditions as wild-type MAM (MAM{sub wt}). Crystals of the L50A mutant are isomorphous with those of MAM{sub wt}, while a new crystal form was obtained for the K201 mutant, belonging to the cubic space group P4{sub 1}32 with unit-cell parameters a = b = c = 181.9 Å. Diffraction data were collected to 3.6 and 2.8 Å resolution from crystals of the MAM L50A and K201A mutants, respectively. Molecular-replacement calculations suggest the presence of two molecules in the asymmetric unit for the MAM K201A mutant crystal, resulting in a V{sub M} of 5.0 Å Da{sup −1} and a solvent content of 75%. An interpretable electron-density map for the MAM K201A mutant crystal was produced using the molecular-replacement method.

X-ray diffraction analysis of LiCu2O2 crystals with additives of silver atoms

International Nuclear Information System (INIS)

Sirotinkin, V. P.; Bush, A. A.; Kamentsev, K. E.; Dau, H. S.; Yakovlev, K. A.; Tishchenko, E. A.

2015-01-01

Silver-containing LiCu 2 O 2 crystals up to 4 × 8 × 8 mm in size were grown by the crystallization of 80(1-x)CuO · 20 x AgNO 3 · 20Li 2 CO 3 (0 ≤ x ≤ 0.5) mixture melt. According to the X-ray spectral and Rietveld X-ray diffraction data, the maximum amount of silver incorporated in the LiCu 2 O 2 structure is about 4 at % relative to the copper content. It was established that silver atoms occupy statistically crystallographic positions of lithium atoms. The incorporation of silver atoms is accompanied by a noticeable increase in parameter c of the LiCu 2 O 2 rhombic unit cell, a slight increase in parameter a, and a slight decrease in parameter b

REVIEW: Optics of globular photonic crystals

Science.gov (United States)

Gorelik, V. S.

2007-05-01

The results of experimental and theoretical studies of the optical properties of globular photonic crystals - new physical objects having a crystal structure with the lattice period exceeding considerably the atomic size, are presented. As globular photonic crystals, artificial opal matrices consisting of close-packed silica globules of diameter ~200 nm were used. The reflection spectra of these objects characterising the parameters of photonic bands existing in these crystals in the visible spectral region are presented. The idealised models of the energy band structure of photonic crystals investigated in the review give analytic dispersion dependences for the group velocity and the effective photon mass in a globular photonic crystal. The characteristics of secondary emission excited in globular photonic crystals by monochromatic and broadband radiation are presented. The results of investigations of single-photon-excited delayed scattering of light observed in globular photonic crystals exposed to cw UV radiation and radiation from a repetitively pulsed copper vapour laser are presented. The possibilities of using globular photonic crystals as active media for lasing in different spectral regions are considered. It is proposed to use globular photonic crystals as sensitive sensors in optoelectronic devices for molecular analysis of organic and inorganic materials by the modern methods of laser spectroscopy. The results of experimental studies of spontaneous and stimulated globular scattering of light are discussed. The conditions for observing resonance and two-photon-excited delayed scattering of light are found. The possibility of accumulation and localisation of the laser radiation energy inside a globular photonic crystal is reported.

Crystallization and preliminary X-ray analysis of LipL32 from Leptospira interrogans serovar Copenhageni

International Nuclear Information System (INIS)

Hauk, Pricila; Guzzo, Cristiane R.; Ho, Paulo L.; Farah, Chuck S.

2009-01-01

Recombinant selenomethionine-labelled LipL32, the major surface protein of pathogenic Leptospira, has been purified and crystallized. Data sets from two crystals were collected, one of which diffracted to 2.25 Å resolution. LipL32 is a major surface protein that is expressed during infection by pathogenic Leptospira. Here, the crystallization of recombinant LipL32 21–272 , which corresponds to the mature LipL32 protein minus its N-terminal lipid-anchored cysteine residue, is described. Selenomethionine-labelled LipL32 21–272 crystals diffracted to 2.25 Å resolution at a synchrotron source. The space group was P3 1 21 or P3 2 21 and the unit-cell parameters were a = b = 126.7, c = 96.0 Å

Cloning, Expression, Purification, Crystallization and Preliminary X-ray Analysis of Mycoplasma Genitalium Protein MG289

Energy Technology Data Exchange (ETDEWEB)

Sippel, K.; Boehlein, S; Sakai, Y; Quirit, J; Agbandje-McKenna, M; Rosser, C; McKenna, R

2009-01-01

Mycoplasma genitalium is a human pathogen that is associated with nongonococcal urethritis in men and cervicitis in women. The cloning, expression, purification and crystallization of the protein MG289 from M. genitalium strain G37 are reported here. Crystals of MG289 diffracted X-rays to 2.8 {angstrom} resolution. The crystals belonged to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 49.7, b = 90.9, c = 176.1 {angstrom}. The diffraction data after processing had an overall R{sub merge} of 8.7%. The crystal structure of Cypl, the ortholog of MG289 from M. hyorhinis, has recently been determined, providing a reasonable phasing model; molecular replacement is currently under way.

Towards true 3D textural analysis; using your crystal mush wisely.

Science.gov (United States)

Jerram, D. A.; Morgan, D. J.; Pankhurst, M. J.

2014-12-01

The crystal cargo that is found in volcanic and plutonic rocks contains a wealth of information about magmatic mush processes, crystallisation history, crystal entrainment and recycling. Phenocryst populations predominantly record episodes of growth/nucleation and bulk geochemical changes within an evolving crystal-melt body. Ante- and xeno-crysts provide useful clues to the nature of mush interaction with wall rock and with principal magma(s). Furthermore, crystal evolutions (core to rim) record pathways through pressure, temperature and compositional space. These can often illustrate complex recycling within systems, describing the plumbing architecture. Understanding this architecture underpins our knowledge of how igneous systems can interact with the crust, grow, freeze, re-mobilise and prime for eruption. Initially, 2D studies produced corrected 3D crystal size distributions to help provide information about nucleation and residence times. It immediately became clear that crystal shape is an important factor in determining the confidence placed upon 3D reconstructions of 2D data. Additionally studies utilised serial sections of medium- to coarse-grain-size populations which allowed 3D reconstruction using modelling software to be improved, since size and shape etc. can be directly constrained. Finally the advent of textural studies using X-ray tomography has revolutionised the way in which we can inspect the crystal cargo in mushy systems, allowing us to image in great detail crystal packing arrangements, 3D CSDs, shapes and orientations etc. The latest most innovative studies use X-ray micro-computed tomography to rapidly characterise chemical populations within the crystal cargo, adding a further dimension to this approach, and implies the ability to untangle magmatic chemical components to better understand their individual and combined evolution. In this contribution key examples of the different types of textural analysis techniques in 2D and 3D

An effect of re-extraction crystallization parameters on physical and chemical properties of AUC

International Nuclear Information System (INIS)

Yahi, Boussad

1990-07-01

This study is concerned with direct cristallization of ammonium uranyl carbonate (AUC) from a uranium loaded organic phase (30% TBP in kerosene), with ammonium carbonate (NH4)2 CO3. The effects of operating conditions (NH4)2 CO3 concentration, flowration residence time, temperature on the physical properties of AUC crystals (particle size distribution, specific area, density..) are reported. All products were identified (both by chemical analysis, X-Ray diffraction) as being ammonium uranyl ratio and (NH4)2 CO3 concentration favor the formation of fine AUC grains and aggregates. This is due mainly to the high concentration of (NH4)+ in the system which leads to a high solution supersaturation and consequently to a rapid formation rate of crystal (germination). The reverse phenomenon is observed at low phase ratio and (NH4)2 CO3 concentration, where germination and crystal growth ara slow and the product is mainly monocrystal. In the intermediate range, a mixture of polycrystal and aggregates is obtained. Residence time and temperature are also shown to have an effect on the processes (the effect of time being more important than temperature)

Crystal field levels of tetravalent actinide ions in actinide dioxides UO2, NpO2 and PuO2

International Nuclear Information System (INIS)

Krupa, J.C.; Gajek, Z.

1991-01-01

Crystal-field parameters resulting from analysis of optical spectroscopy and neutron diffraction data recorded on UO 2 and NpO 2 as well as ab-initio calculated parameters were used to calculate the crystal-field eigenfunctions and eigenvalues for the J ground-state manifold of U 4+ , Np 4+ and Pu 4+ in UO 2 , NpO 2 and PuO 2

Purification, crystallization and preliminary X-ray analysis of urease from jack bean (Canavalia ensiformis)

International Nuclear Information System (INIS)

Balasubramanian, Anuradha; Ponnuraj, Karthe

2009-01-01

Jack bean urease was purified and crystallized and X-ray diffraction data were collected to 2.05 Å resolution. Plant urease is a seed protein that is common in most legumes. It is also common in many bacteria and fungi and several species of yeast. Urease allows organisms to use exogenous and internally generated urea as a nitrogen source by catalyzing the hydrolysis of urea to ammonia and carbon dioxide. Urease from jack bean meal was purified to electrophoretic homogeneity using a series of steps involving acetone precipitation and size-exclusion and ion-exchange chromatography. The jack bean urease was crystallized and the resulting crystals diffracted to 2.05 Å resolution using synchrotron radiation. The crystals belonged to the hexagonal space group P6 3 22, with unit-cell parameters a = b = 138.57, c = 198.36 Å

Structural elucidation and physicochemical properties of an organic NLO crystal: 4-Nitrotoluene-2-sulphonic acid dihydrate

Science.gov (United States)

Sangeetha, K.; Guru Prasad, L.; Mathammal, R.

2018-03-01

4-nitrotoluene-2-sulphonic acid dihydrate single crystals have been developed using slow evaporation technique in methanol. Lattice parameters of the NTSAD crystal have been calculated and it confirms the grown material. The intermolecular interactions are studied from the 3D Hirshfeld surface analysis and 2D fingerprint plots. The NMR spectral analysis has been carried out to confirm the molecular structure of the grown material. Optical properties have been obtained from UV-VIS spectral analysis and photoluminescence studies. Frequency conversion property of the NTSAD crystal was investigated with the aid of Kurtz and Perry method.

Ultra compact spectrometer apparatus and method using photonic crystals

Science.gov (United States)

Ting, David Z. (Inventor); Hill, Cory J. (Inventor); Bandara, Sumith V. (Inventor); Gunapala, Sarath D. (Inventor)

2009-01-01

The present invention is directed to methods of photonic crystal formation, and to methods and apparatus for using such photonic crystals, particularly in conjunction with detector arrays. Photonic crystal parameters and detector array parameters are compared to optimize the selection and orientation of a photonic crystal shape. A photonic crystal is operatively positioned relative to a plurality of light sensors. The light sensors can be separated by a pitch distance and positioned within one half of the pitch distance of an exit surface of the photonic crystals.

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

Energy Technology Data Exchange (ETDEWEB)

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

2015-03-20

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

Crystallization and preliminary X-ray analysis of tubulin-folding cofactor A from Arabidopsis thaliana

International Nuclear Information System (INIS)

Lu, Lu; Nan, Jie; Mi, Wei; Wei, Chun-Hong; Li, Lan-Fen; Li, Yi

2010-01-01

Tubulin-folding cofactor A from A. thaliana has been crystallized and preliminarily analyzed using X-ray diffraction. Tubulin-folding cofactor A (TFC A) is a molecular post-chaperonin that is involved in the β-tubulin-folding pathway. It has been identified in many organisms including yeasts, humans and plants. In this work, Arabidopsis thaliana TFC A was expressed in Escherichia coli and purified to homogeneity. After thrombin cleavage, a well diffracting crystal was obtained by the sitting-drop vapour-diffusion method at 289 K. The crystal diffracted to 1.6 Å resolution using synchrotron radiation and belonged to space group I4 1 , with unit-cell parameters a = 55.0, b = 55.0, c = 67.4 Å

Crystallization and preliminary crystallographic analysis of an octaketide-producing plant type III polyketide synthase

Energy Technology Data Exchange (ETDEWEB)

Morita, Hiroyuki [Mitsubishi Kagaku Institute of Life Sciences (MITILS), 11 Minamiooya, Machida, Tokyo 194-8511 (Japan); Kondo, Shin; Kato, Ryohei [Innovation Center Yokohama, Mitsubishi Chemical Corporation, 1000 Kamoshida, Aoba, Yokohama, Kanagawa 227-8502 (Japan); Wanibuchi, Kiyofumi; Noguchi, Hiroshi [School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526 (Japan); Sugio, Shigetoshi, E-mail: sugio.shigetoshi@mw.m-kagaku.co.jp [Innovation Center Yokohama, Mitsubishi Chemical Corporation, 1000 Kamoshida, Aoba, Yokohama, Kanagawa 227-8502 (Japan); Abe, Ikuro, E-mail: sugio.shigetoshi@mw.m-kagaku.co.jp [School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526 (Japan); PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012 (Japan); Kohno, Toshiyuki, E-mail: sugio.shigetoshi@mw.m-kagaku.co.jp [Mitsubishi Kagaku Institute of Life Sciences (MITILS), 11 Minamiooya, Machida, Tokyo 194-8511 (Japan)

2007-11-01

Octaketide synthase from A. arborescens has been overexpressed in E. coli, purified and crystallized. Diffraction data have been collected to 2.6 Å. Octaketide synthase (OKS) from Aloe arborescens is a plant-specific type III polyketide synthase that produces SEK4 and SEK4b from eight molecules of malonyl-CoA. Recombinant OKS expressed in Escherichia coli was crystallized by the hanging-drop vapour-diffusion method. The crystals belonged to space group I422, with unit-cell parameters a = b = 110.2, c = 281.4 Å, α = β = γ = 90.0°. Diffraction data were collected to 2.6 Å resolution using synchrotron radiation at BL24XU of SPring-8.

Purification, crystallization and preliminary X-ray diffraction studies of parakeet (Psittacula krameri) haemoglobin

International Nuclear Information System (INIS)

Jaimohan, S. M.; Naresh, M. D.; Arumugam, V.; Mandal, A. B.

2009-01-01

Parakeet (Psittacula krameri) haemoglobin has been purified and crystallized under low salt buffered conditions. Preliminary analysis of the crystal that belonged to monoclinic system (C2) is reported. Birds often show efficient oxygen management in order to meet the special demands of their metabolism. However, the structural studies of avian haemoglobins (Hbs) are inadequate for complete understanding of the mechanism involved. Towards this end, purification, crystallization and preliminary X-ray diffraction studies have been carried out for parakeet Hb. Parakeet Hb was crystallized as the met form in low-salt buffered conditions after extracting haemoglobin from crude blood by microcentrifugation and purifying the sample by column chromatography. Good-quality crystals were grown from 10% PEG 3350 and a crystal diffracted to about 2.8 Å resolution. Preliminary diffraction data showed that the Hb crystal belonged to the monoclinic system (space group C2), with unit-cell parameters a = 110.68, b = 64.27, c = 56.40 Å, β = 109.35°. Matthews volume analysis indicated that the crystals contained a half-tetramer in the asymmetric unit

Crystallization and preliminary X-ray analysis of the flagellar motor `brake' molecule YcgR with c-di-GMP from Escherichia coli.

Science.gov (United States)

Hou, Yanjie; Li, De Feng; Wang, Da Cheng

2013-06-01

In Escherichia coli and Salmonella enterica, bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP), a ubiquitous bacterial second-messenger molecule that participates in many cellular processes, can regulate flagellar motor speed and reduce cell swimming velocity by binding to the PilZ-containing protein YcgR. Here, the crystallization and preliminary X-ray crystallographic analysis of YcgR with c-di-GMP are reported. The crystals diffracted to 2.3 Å resolution and belonged to space group R3:H, with unit-cell parameters a = b = 93.96, c = 109.61 Å. The asymmetric unit appeared to contain one subunit with a Matthews coefficient of 3.21 Å(3) Da(-1). The results reported here provide a sound basis for solving the crystal structure of YcgR with c-di-GMP and revealing its structure-function relationship based on the three-dimensional structure.

Piezoelectric Ca{sub 3}NbGa{sub 3}Si{sub 2}O{sub 14} crystal: crystal growth, piezoelectric and acoustic properties

Energy Technology Data Exchange (ETDEWEB)

Roshchupkin, Dmitry; Emelin, Evgenii [Russian Academy of Sciences, Institute of Microelectronics Technology and High-Purity Materials, Chernogolovka, Moscow District (Russian Federation); National University of Science and Technology MISiS, Moscow (Russian Federation); Ortega, Luc [Univ. Paris-Sud, CNRS, UMR 8502, Laboratoire de Physique des Solides, Orsay Cedex (France); Plotitcyna, Olga; Irzhak, Dmitry [Russian Academy of Sciences, Institute of Microelectronics Technology and High-Purity Materials, Chernogolovka, Moscow District (Russian Federation); Erko, Alexei; Zizak, Ivo; Vadilonga, Simone [Helmholtz-Zentrum Berlin fuer Materialien und Energie GmbH, Institute for Nanometre Optics and Technology, Berlin (Germany); Buzanov, Oleg [FOMOS Materials Co., Moscow (Russian Federation); Leitenberger, Wolfram [Universitaet Potsdam Institut fuer Physik, Potsdam (Germany)

2016-08-15

Ca{sub 3}NbGa{sub 3}Si{sub 2}O{sub 14} (CNGS), a five-component crystal of lanthanum-gallium silicate group, was grown by the Czochralski method. The parameters of the elementary unit cell of the crystal were measured by powder diffraction. The independent piezoelectric strain coefficients d{sub 11} and d{sub 14} were determined by the triple-axis X-ray diffraction in the Bragg and Laue geometries. Excitation and propagation of surface acoustic waves (SAW) were studied by high-resolution X-ray diffraction at BESSY II synchrotron radiation source. The velocity of SAW propagation and power flow angles in the Y-, X- and yxl/+36 {sup circle} -cuts of the CNGS crystal were determined from the analysis of the diffraction spectra. The CNGS crystal was found practically isotropic by its acoustic properties. (orig.)

Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations.

Science.gov (United States)

van de Streek, Jacco; Neumann, Marcus A

2010-10-01

This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095 Å (0.084 Å for the 225 ordered structures). R.m.s. Cartesian displacements above 0.25 A either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect.

Overexpression, crystallization and preliminary X-ray crystallographic analysis of Pseudomonas aeruginosa MnmE, a GTPase involved in tRNA modification

International Nuclear Information System (INIS)

Lee, Hyung Ho; Suh, Se Won

2010-01-01

MnmE from P. aeruginosa was crystallized and X-ray diffraction data were collected to 2.69 Å resolution. MnmE, an evolutionarily conserved GTPase, is involved in modification of the uridine base (U34) at the wobble position of certain tRNAs. Previous crystal structures of MnmE suggest that it is a dimer with considerable conformational flexibility. To facilitate structural comparisons among MnmE proteins, structural analysis of MnmE from Pseudomonas aeruginosa encoded by the PA5567 gene was initiated. It was overexpressed in Escherichia coli and crystallized at 297 K using a reservoir solution consisting of 100 mM sodium ADA pH 6.5, 12%(w/v) polyethylene glycol 4000, 100 mM lithium sulfate, 2%(v/v) 2-propanol and 2.5 mM dithiothreitol. X-ray diffraction data were collected to 2.69 Å resolution. The crystals belonged to the orthorhombic space group C222 1 , with unit-cell parameters a = 96.74, b = 204.66, c = 120.90 Å. Two monomers were present in the asymmetric unit, resulting in a crystal volume per protein mass (V M ) of 2.99 Å 3 Da −1 and a solvent content of 58.8%

Growth and spectroscopic, thermodynamic and nonlinear optical studies of L-threonine phthalate crystal

Science.gov (United States)

Theras, J. Elberin Mary; Kalaivani, D.; Jayaraman, D.; Joseph, V.

2015-10-01

L-threonine phthalate (LTP) single crystal has been grown using a solution growth technique at room temperature. Single crystal X-ray diffraction analysis reveals that LTP crystallizes in monoclinic crystal system with space group C2/c. The optical absorption studies show that the crystal is transparent in the entire visible region with a cut-off wavelength 309 nm. The optical band gap is found to be 4.05 eV. The functional groups of the synthesized compound have been identified by FTIR spectral analysis. The functional groups present in the material were also confirmed by FT-RAMAN spectroscopy. Surface morphology and the presence of various elements were studied by SEM-EDAX analysis. The thermal stability of LTP single crystal has been analyzed by TGA/DTA studies. The thermodynamic parameters such as activation energy, entropy, enthalpy and Gibbs free energy were determined for the grown material using TG data and Coats-Redfern relation. Since the grown crystal is centrosymmetric, Z-Scan studies were carried out for analyzing the third order nonlinear optical property. The nonlinear absorption coefficient, nonlinear refractive index and susceptibility have been measured using Z-Scan technique.

Expression, purification, crystallization and preliminary X-ray diffraction analysis of rhesus macaque CD8αα homodimer

International Nuclear Information System (INIS)

Zong, Lili; Chen, Yong; Yan, Jinghua; Zhang, Jianhua

2010-01-01

CD8α exodomain protein, a crucial immune-system factor in rhesus macaque (M. mulatta), one of the best animal models for vaccine design, was assembled and crystallized. The full structure data will contribute to future studies of immune responses in rhesus macaques. As a T-cell co-receptor, CD8 binds to MHC class I molecules and plays a pivotal role in the activation of cytotoxic T lymphocytes. To date, structures of CD8 have been solved for two different mammals: human and mouse. The infection of rhesus macaques (Macaca mulatta) by simian immunodeficiency virus (SIV) is the best animal model for studying HIV. In this study, the rhesus macaque CD8 (rCD8) αα homodimer was obtained and rCD8α exodomain protein crystals were successfully obtained for further structural analysis. Diffraction data were collected to a resolution of 2.4 Å. The crystal belonged to space group P2 1 2 1 2 1 , with unit-cell parameters a = 46.52, b = 56.28, c = 82.40 Å. These data will facilitate further studies on the structural differences between these CD8 structures and the cellular immune responses of rhesus macaque

Physicochemical properties of dimethylammonium p-nitrophenolate– p-nitrophenol: A nonlinear optical crystal

International Nuclear Information System (INIS)

Rathika, A.; Prasad, L. Guru; Raman, R. Ganapathi

2016-01-01

Single crystals of Dimethylammonium p-nitrophenolate–p-nitrophenol have been grown from aqueous solution by slow evaporation solution growth technique. Unit cell parameters of the grown crystal were confirmed by single crystal X-ray diffraction analysis and the synthesized compound is crystallized in monoclinic system. Various functional groups and their vibrational frequencies were recognized from the FT-IR and FT-Raman spectrum. Thermal stability of the crystal was examined by recording the TGA/DTA curve. The grown crystal has wider transparency nature in the visible region and the lower cut-off wavelength is found at 465 nm. Mechanical property of the crystal was studied by analyzing the Vicker's microhardness measurements. The fluorescence emission from the crystal is observed at 350 nm which arise due to the presence of aromatic ring. Relative SHG conversion efficiency of the grown crystal is about 0.59 times that of KDP.

Physicochemical properties of dimethylammonium p-nitrophenolate– p-nitrophenol: A nonlinear optical crystal

Energy Technology Data Exchange (ETDEWEB)

Rathika, A. [Department of Physics, Noorul Islam Centre for Higher Education, Noorul Islam University, Kumaracoil 629 180 (India); Prasad, L. Guru [Departemnt of Science & Humanities, M. Kumarasamy College of Engineering, Karur (India); Raman, R. Ganapathi, E-mail: ganapathiraman83@gmail.com [Department of Physics, Noorul Islam Centre for Higher Education, Noorul Islam University, Kumaracoil 629 180 (India)

2016-03-15

Single crystals of Dimethylammonium p-nitrophenolate–p-nitrophenol have been grown from aqueous solution by slow evaporation solution growth technique. Unit cell parameters of the grown crystal were confirmed by single crystal X-ray diffraction analysis and the synthesized compound is crystallized in monoclinic system. Various functional groups and their vibrational frequencies were recognized from the FT-IR and FT-Raman spectrum. Thermal stability of the crystal was examined by recording the TGA/DTA curve. The grown crystal has wider transparency nature in the visible region and the lower cut-off wavelength is found at 465 nm. Mechanical property of the crystal was studied by analyzing the Vicker's microhardness measurements. The fluorescence emission from the crystal is observed at 350 nm which arise due to the presence of aromatic ring. Relative SHG conversion efficiency of the grown crystal is about 0.59 times that of KDP.

Crystallization and preliminary crystallographic analysis of Abp, a GH27 β-l-arabinopyranosidase from Geobacillus stearothermophilus

International Nuclear Information System (INIS)

Lansky, Shifra; Salama, Rachel; Solomon, Vered H.; Belrhali, Hassan; Shoham, Yuval; Shoham, Gil

2013-01-01

A GH27 arabinopyranosidase from G. stearothermophilus (Abp) has been crystallized in the primitive orthorhombic space group P2 1 2 1 2 1 . Full diffraction data sets have been measured for the wild-type enzyme and its D197A catalytic mutant to maximal resolutions of 2.28 and 2.30 Å, respectively, for use in a detailed three-dimensional structural analysis of the Abp protein. Geobacillus stearothermophilus T-6 is a thermophilic soil bacterium that possesses an extensive system for the utilization of hemicellulose. The bacterium produces a small number of endo-acting extracellular enzymes that cleave high-molecular-weight hemicellulolytic polymers into short decorated oligosaccharides, which are further hydrolysed into the respective sugar monomers by a battery of intracellular glycoside hydrolases. One of these intracellular processing enzymes is β-l-arabinopyranosidase (Abp), which is capable of removing β-l-arabinopyranose residues from naturally occurring arabino-polysaccharides. As arabino-polymers constitute a significant part of the hemicellulolytic content of plant biomass, their efficient enzymatic degradation presents an important challenge for many potential biotechnological applications. This aspect has led to an increasing interest in the biochemical characterization and structural analysis of this and related hemicellulases. Abp from G. stearothermophilus T-6 has recently been cloned, overexpressed, purified, biochemically characterized and crystallized in our laboratory, as part of its complete structure–function study. The best crystals obtained for this enzyme belonged to the primitive orthorhombic space group P2 1 2 1 2 1 , with average unit-cell parameters a = 107.7, b = 202.2, c = 287.3 Å. Full diffraction data sets to 2.3 Å resolution have been collected for both the wild-type enzyme and its D197A catalytic mutant from flash-cooled crystals at 100 K, using synchrotron radiation. These data are currently being used for a high

Diffusion in Coulomb crystals.

Science.gov (United States)

Hughto, J; Schneider, A S; Horowitz, C J; Berry, D K

2011-07-01

Diffusion in Coulomb crystals can be important for the structure of neutron star crusts. We determine diffusion constants D from molecular dynamics simulations. We find that D for Coulomb crystals with relatively soft-core 1/r interactions may be larger than D for Lennard-Jones or other solids with harder-core interactions. Diffusion, for simulations of nearly perfect body-centered-cubic lattices, involves the exchange of ions in ringlike configurations. Here ions "hop" in unison without the formation of long lived vacancies. Diffusion, for imperfect crystals, involves the motion of defects. Finally, we find that diffusion, for an amorphous system rapidly quenched from Coulomb parameter Γ=175 to Coulomb parameters up to Γ=1750, is fast enough that the system starts to crystalize during long simulation runs. These results strongly suggest that Coulomb solids in cold white dwarf stars, and the crust of neutron stars, will be crystalline and not amorphous.

Purification, crystallization and preliminary X-ray diffraction analysis of disease-related mutants of p97

International Nuclear Information System (INIS)

Tang, Wai-Kwan; Li, Dongyang; Esser, Lothar; Xia, Di

2009-01-01

Mutations in the human AAA+ protein p97 cause a disease in humans called IBMPFD. How these mutations affect the structure and function of p97 is unknown. Here, the crystallization of three disease-related mutants of p97 in the presence of ATPγS are reported. The human type II AAA+ protein p97 participates in various cellular activities, presumably through its involvement in the ubiquitin–proteasome degradation pathway. Mutations in p97 have been implicated in patients with inclusion-body myopathy associated with Paget’s disease of the bone and frontotemporal dementia (IBMPFD). In this work, three mutant p97 N-D1 fragments, R86A, R95G and R155H, were crystallized in the presence of ATPγS with PEG 3350 as a main precipitant, yielding two different crystal forms. The R155H mutant crystal belonged to space group R3, with unit-cell parameters in the hexagonal setting of a = b = 134.2, c = 182.9 Å, and was merohedrally twinned, with an estimated twin fraction of 0.34. The crystals of the R86A and R95G mutants belonged to space group P1, with similar unit-cell parameters of a = 90.89, b = 102.6, c = 107.2 Å, α = 97.5, β = 90.6, γ = 91.5° and a = 92.76, b = 103.7, c = 107.7 Å, α = 97.7, β = 91.9, γ = 89.7°, respectively

Crystallization and preliminary crystallographic analysis of a putative glucokinase/hexokinase from Thermus thermophilus

International Nuclear Information System (INIS)

Nakamura, Tsutomu; Kashima, Yasuhiro; Mine, Shouhei; Oku, Takashi; Uegaki, Koichi

2011-01-01

In this study, a putative glucokinase/hexokinase from T. thermophilus was purified and crystallized. Diffraction data were collected and processed to 2.02 Å resolution. Glucokinase/hexokinase catalyzes the phosphorylation of glucose to glucose 6-phosphate, which is the first step of glycolysis. The open reading frame TTHA0299 of the extreme thermophile Thermus thermophilus encodes a putative glucokinase/hexokinase which contains the consensus sequence for proteins from the repressors, open reading frames and sugar kinases family. In this study, the glucokinase/hexokinase from T. thermophilus was purified and crystallized using polyethylene glycol 8000 as a precipitant. Diffraction data were collected and processed to 2.02 Å resolution. The crystal belonged to space group P2 1 , with unit-cell parameters a = 70.93, b = 138.14, c = 75.16 Å, β = 95.41°

Expression, crystallization and preliminary X-ray crystallographic analysis of human agmatinase

International Nuclear Information System (INIS)

Kim, Kyoung Hoon; Ahn, Hyung Jun; Kim, Do Jin; Lee, Hyung Ho; Ha, Jun-Yong; Kim, Hye-Kyung; Yoon, Hye-Jin; Suh, Se Won

2005-01-01

Human agmatinase (Ala36–Val352) was overexpressed and crystallized, and X-ray diffraction data were collected to 2.49 Å. Agmatine, which results from the decarboxylation of l-arginine by arginine decarboxylase, is a metabolic intermediate in the biosynthesis of putresine and higher polyamines (spermidine and spermine). Recent studies indicate that agmatine can have several important biochemical effects in humans, ranging from effects on the central nervous system to cell proliferation in cancer and viral replication. Agmatinase catalyses the hydrolysis of agmatine to putresine and urea and is a major target for drug action and development. The human agmatinase gene encodes a 352-residue protein with a putative mitochondrial targeting sequence at the N-terminus. Human agmatinase (residues Ala36–Val352) has been overexpressed as a fusion with both N- and C-terminal purification tags in Escherichia coli and crystallized in the presence of Mn 2+ and 1,6-diaminohexane at 297 K using polyethylene glycol 4000 as a precipitant. X-ray diffraction data were collected at 100 K to 2.49 Å from a flash-frozen crystal. The crystals are tetragonal, belonging to space group P4 2 , with unit-cell parameters a = b = 114.54, c = 125.65 Å, α = β = γ = 90°. Three monomers are likely to be present in the asymmetric unit, giving a crystal volume per protein weight (V M ) of 3.66 Å 3 Da −1 and a solvent content of 66.4%

Mathematical modeling and fuzzy availability analysis for serial processes in the crystallization system of a sugar plant

Science.gov (United States)

Aggarwal, Anil Kr.; Kumar, Sanjeev; Singh, Vikram

2017-03-01

The binary states, i.e., success or failed state assumptions used in conventional reliability are inappropriate for reliability analysis of complex industrial systems due to lack of sufficient probabilistic information. For large complex systems, the uncertainty of each individual parameter enhances the uncertainty of the system reliability. In this paper, the concept of fuzzy reliability has been used for reliability analysis of the system, and the effect of coverage factor, failure and repair rates of subsystems on fuzzy availability for fault-tolerant crystallization system of sugar plant is analyzed. Mathematical modeling of the system is carried out using the mnemonic rule to derive Chapman-Kolmogorov differential equations. These governing differential equations are solved with Runge-Kutta fourth-order method.

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

Energy Technology Data Exchange (ETDEWEB)

Murata, Kenji [Department of Animal Science, University of California, Davis 95616 (United States); Fisher, Andrew J. [Department of Chemistry, University of California, Davis 95616 (United States); Hedrick, Jerry L., E-mail: jlhedrick@ucdavis.edu [Department of Animal Science, University of California, Davis 95616 (United States)

2007-05-01

The 24 kDa egg lectin of Chinook salmon (Oncorhynchus tshawytscha) was purified by affinity chromatography from salmon eggs and crystallized by the hanging-drop vapor-diffusion method using 15/4 EO/OH (pentaerythritol ethoxylate) as a precipitant. The 24 kDa egg lectin of Chinook salmon (Oncorhynchus tshawytscha) is released from the egg during the cortical reaction. The lectin functions in blocking polyspermy during the fertilization process. The egg lectin was purified by affinity chromatography from salmon eggs and crystallized by the hanging-drop vapor-diffusion method using 15/4 EO/OH (pentaerythritol ethoxylate) as a precipitant. The crystal diffracted synchrotron-radiation X-rays to 1.63 Å resolution. The crystal belongs to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 93.0, b = 73.6, c = 113.6 Å, α = 90, β = 92.82, γ = 90°. The crystal is likely to contain eight molecules in the asymmetric unit (V{sub M} = 2.3 Å{sup 3} Da{sup −1}), corresponding to a solvent content of 45.5%. A self-rotation function suggests an arrangement with 222 point symmetry within the asymmetric unit.

Liquid crystals of carbon nanotubes and graphene.

Science.gov (United States)

Zakri, Cécile; Blanc, Christophe; Grelet, Eric; Zamora-Ledezma, Camilo; Puech, Nicolas; Anglaret, Eric; Poulin, Philippe

2013-04-13

Liquid crystal ordering is an opportunity to develop novel materials and applications with spontaneously aligned nanotubes or graphene particles. Nevertheless, achieving high orientational order parameter and large monodomains remains a challenge. In addition, our restricted knowledge of the structure of the currently available materials is a limitation for fundamental studies and future applications. This paper presents recent methodologies that have been developed to achieve large monodomains of nematic liquid crystals. These allow quantification and increase of their order parameters. Nematic ordering provides an efficient way to prepare conductive films that exhibit anisotropic properties. In particular, it is shown how the electrical conductivity anisotropy increases with the order parameter of the nematic liquid crystal. The order parameter can be tuned by controlling the length and entanglement of the nanotubes. In the second part of the paper, recent results on graphene liquid crystals are reported. The possibility to obtain water-based liquid crystals stabilized by surfactant molecules is demonstrated. Structural and thermodynamic characterizations provide indirect but statistical information on the dimensions of the graphene flakes. From a general point of view, this work presents experimental approaches to optimize the use of nanocarbons as liquid crystals and provides new methodologies for the still challenging characterization of such materials.

Crystallization and preliminary X ray analysis of nucleoside diphosphate kinase 1 from T. cruzi

International Nuclear Information System (INIS)

Gomez Barroso, J.A.; Aguilar, C.F.; Miranda, M.R.; Pereira, C.A.

2009-01-01

Introduction: Trypanosoma cruzi is the etiologic agent of Chagas disease. The Nucleoside diphosphate kinases (NDPKs) are enzymes involved in energy management and nucleoside balance in the cell. T. cruzi TcNDPK1, a canonical isoform. The objective of this work is obtaining protein's crystals, diffract and process the data for tridimensional structure resolution. Materials and Methods: TcNDPK1 was expressed in E. coli as a fusion protein with Nterminal His-tag. TcNDPK1 was overexpressed and purified by FPLC. Crystallization was assayed by sitting drop and hanging drop vapor diffusion method. Crystals was frozen and diffracted on synchrotron x-ray radiation in Campinas (Brasil). The data set collected was reduced and merged using MOSFLM and SCALA programs. Results and Discussion: His-TcNDPK was overexpressed, purified and crystallized. The crystals are diffracted and collected the data to 3.5A. The crystals belong to the trigonal space group P3, with unit cell parameters a=127.94, b=127.84, c=275.49. Structure determination is under way. These results will provide relevant information that could be the first step in rational drug design for treating Chagas disease.(authors)

Crystallization of mouse S-adenosyl-l-homocysteine hydrolase

International Nuclear Information System (INIS)

Ishihara, Masaaki; Kusakabe, Yoshio; Ohsumichi, Tsuyoshi; Tanaka, Nobutada; Nakanishi, Masayuki; Kitade, Yukio; Nakamura, Kazuo T.

2010-01-01

Mouse S-adenosyl-l-homocysteine hydrolase has been crystallized in the presence of the reaction product adenosine. Diffraction data to 1.55 Å resolution were collected using synchrotron radiation. S-Adenosyl-l-homocysteine hydrolase (SAHH; EC 3.3.1.1) catalyzes the reversible hydrolysis of S-adenosyl-l-homocysteine to adenosine and l-homocysteine. For crystallographic investigations, mouse SAHH (MmSAHH) was overexpressed in bacterial cells and crystallized using the hanging-drop vapour-diffusion method in the presence of the reaction product adenosine. X-ray diffraction data to 1.55 Å resolution were collected from an orthorhombic crystal form belonging to space group I222 with unit-cell parameters a = 100.64, b = 104.44, c = 177.31 Å. Structural analysis by molecular replacement is in progress

Uncertainty analysis of flexible rotors considering fuzzy parameters and fuzzy-random parameters

Directory of Open Access Journals (Sweden)

Fabian Andres Lara-Molina

Full Text Available Abstract The components of flexible rotors are subjected to uncertainties. The main sources of uncertainties include the variation of mechanical properties. This contribution aims at analyzing the dynamics of flexible rotors under uncertain parameters modeled as fuzzy and fuzzy random variables. The uncertainty analysis encompasses the modeling of uncertain parameters and the numerical simulation of the corresponding flexible rotor model by using an approach based on fuzzy dynamic analysis. The numerical simulation is accomplished by mapping the fuzzy parameters of the deterministic flexible rotor model. Thereby, the flexible rotor is modeled by using both the Fuzzy Finite Element Method and the Fuzzy Stochastic Finite Element Method. Numerical simulations illustrate the methodology conveyed in terms of orbits and frequency response functions subject to uncertain parameters.

Purification, crystallization and preliminary X-ray analysis of l-sorbose reductase from Gluconobacter frateurii complexed with l-sorbose or NADPH

International Nuclear Information System (INIS)

Kubota, Keiko; Nagata, Koji; Miyazono, Ken-ichi; Toyama, Hirohide; Matsushita, Kazunobu; Tanokura, Masaru

2009-01-01

NADPH-dependent l-sorbose reductase from G. frateurii (SR) was expressed, purified and crystallized with l-sorbose or NADPH using the sitting-drop vapour-diffusion method. Crystals of the SR–l-sorbose complex and SR–NADPH complex diffracted X-rays to 2.38 and 1.90 Å resolution, respectively. NADPH-dependent l-sorbose reductase (SR) from Gluconobacter frateurii was expressed in Escherichia coli, purified and crystallized with l-sorbose or NADPH using the sitting-drop vapour-diffusion method at 293 K. Crystals of the SR–l-sorbose complex and the SR–NADPH complex were obtained using reservoir solutions containing PEG 2000 or PEG 400 as precipitants and diffracted X-rays to 2.38 and 1.90 Å resolution, respectively. The crystal of the SR–l-sorbose complex belonged to space group C222 1 , with unit-cell parameters a = 124.2, b = 124.1, c = 60.8 Å. The crystal of the SR–NADPH complex belonged to space group P2 1 , with unit-cell parameters a = 124.3, b = 61.0, c = 124.5 Å, β = 89.99°. The crystals contained two and eight molecules, respectively, in the asymmetric unit

Purification, crystallization and preliminary X-ray analysis of a thermostable glycoside hydrolase family 43 β-xylosidase from Geobacillus thermoleovorans IT-08

International Nuclear Information System (INIS)

Rohman, Ali; Oosterwijk, Niels van; Kralj, Slavko; Dijkhuizen, Lubbert; Dijkstra, Bauke W.; Puspaningsih, Ni Nyoman Tri

2007-01-01

The β-xylosidase was crystallized using PEG 6000 as precipitant. 5% PEG 6000 yielded bipyramid-shaped tetragonal crystals diffracting to 1.55 Å resolution, and 13% PEG 6000 gave rectangular monoclinic crystals diffracting to 1.80 Å resolution. The main enzymes involved in xylan-backbone hydrolysis are endo-1,4-β-xylanase and β-xylosidase. β-Xylosidase converts the xylo-oligosaccharides produced by endo-1,4-β-xylanase into xylose monomers. The β-xylosidase from the thermophilic Geobacillus thermoleovorans IT-08, a member of glycoside hydrolase family 43, was crystallized at room temperature using the hanging-drop vapour-diffusion method. Two crystal forms were observed. Bipyramid-shaped crystals belonging to space group P4 3 2 1 2, with unit-cell parameters a = b = 62.53, c = 277.4 Å diffracted to 1.55 Å resolution. The rectangular crystals belonged to space group P2 1 , with unit-cell parameters a = 57.94, b = 142.1, c = 153.9 Å, β = 90.5°, and diffracted to 1.80 Å resolution

Crystallization and preliminary X-ray diffraction analysis of a tRNASer acceptor-stem microhelix

International Nuclear Information System (INIS)

Förster, Charlotte; Krauss, Norbert; Brauer, Arnd B. E.; Szkaradkiewicz, Karol; Brode, Svenja; Hennig, Klaus; Fürste, Jens P.; Perbandt, Markus; Betzel, Christian; Erdmann, Volker A.

2006-01-01

In order to investigate tRNA identity elements, an elongator tRNA Ser acceptor-stem helix was crystallized and a data set was collected to 1.8 Å resolution aiming at a comparison with the corresponding region in suppressor tRNA Sec . In order to understand elongator tRNA Ser and suppressor tRNA Sec identity elements, the respective acceptor-stem helices have been synthesized and crystallized in order to analyse and compare their structures in detail at high resolution. The synthesis, crystallization and preliminary X-ray diffraction results for a seven-base-pair tRNA Ser acceptor-stem helix are presented here. Diffraction data were collected to 1.8 Å, applying synchrotron radiation and cryogenic cooling. The crystals belong to the monoclinic space group C2, with unit-cell parameters a = 36.14, b = 38.96, c = 30.81 Å, β = 110.69°

A crystal barrel

CERN Multimedia

2007-01-01

The production of crystals for the barrel of the CMS electromagnetic calorimeter has been completed. This is an important milestone for the experiment, which received the last of its 62,960 crystals on 9 March. The members of the team responsible for the crystal acceptance testing at CERN display the last crystal for the CMS electromagnetic calorimeter barrel. From left to right: Igor Tarasov, Etiennette Auffray and Hervé Cornet.One of the six machines specially developed to measure 67 different parameters on each crystal. Igor Tarasov is seen inserting the last batch of crystals into the machine. The last of the 62,960 CMS barrel crystals arrived at CERN on 9 March. Once removed from its polystyrene protection, this delicate crystal, like thousands of its predecessors, will be inserted into the last of the 36 supermodules of the barrel electromagnetic calorimeter in a few days' time. This marks the end of an important chapter in an almost 15-year-long journey by the CMS crystals team, some of whose member...

Single-crystal growth of ceria-based materials

International Nuclear Information System (INIS)

Ulbrich, Gregor

2015-01-01

In this work it could be shown that Skull-Melting is a suitable method for growing ceria single crystals. Twenty different ceria-based single crystals could be manufactured. It was possible to dope ceria single crystals with Gd, Sm, Y, Zr, Ti, Ta, and Pr in different concentrations. Also co-doping with the named metals was realized. However, there remain some problems for growing ceria-based single crystals by Skull-Melting. As ignition metal zirconium was used because no ceria-based material works well. For that reason all single crystals show small zirconium contamination. Another problem is the formation of oxygen by the heat-induced reduction of ceria during the melting process. Because of that the skull of sintered material is often destroyed by gas pressure. This problem had to be solved individually for every single crystal. The obtained single crystals were characterized using different methods. To ensure the single crystal character the y were examined by Laue diffraction. All manufactured crystals are single crystals. Also powder diffraction patterns of the milled and oxidized samples were measured. For the determination of symmetry and metric the structural parameters were analyzed by the Rietveld method. All synthesized materials crystallize in space group Fm-3m known from calcium fluoride. The cubic lattice parameter a was determined for all crystals. In the case of series with different cerium and zirconium concentrations a linear correlation between cerium content and cubic lattice parameter was detected. The elemental composition was determined by WDX. All crystals show a homogeneous elemental distribution. The oxygen content was calculated because the WDX method isn't useful for determination.

Analysis of phase transitions and crystal structures of novel benzothiophene derivatives

Science.gov (United States)

Zhang, Shuo

Although single crystal X-ray diffraction remains the most important technique for analyzing periodically ordered structures at atomic resolution, single crystal X-ray diffraction of organic macromolecules is challenged by difficulty in growing single crystals of desired size and quality. Electron crystallography of organic macromolecules, on the other hand, is limited by image resolution due to radiation damage and highly dependent on high-resolution instrumentation. Novel alkylated benzothiophene derivatives synthesized previously can be readily fabricated into semiconductor devices for various applications (photodetectors, explosive sensors, field-effect transistors, light-emitting diodes, etc.) via solution process. The object of this research is to identify phase transitions of organic macromolecules of this kind via differential scanning calorimetry and temperature-resolved wide angle X-ray diffraction, and to determine their lattice parameters and space groups by reconstruction of their reciprocal space via transmission electron microscopy/selected area electron diffraction followed by refinement with X-ray diffraction, supplemented by polarized light microscopy. Computer simulation was performed to rationalize the molecular packing schemes, so as to understand the origin of their electronic performance from crystallographic perspective.

Crystallization and preliminary crystallographic analysis of human Ca2+-loaded calbindin-D28k

International Nuclear Information System (INIS)

Zhang, Chang; Sun, Yuna; Wang, Wei; Zhang, Yan; Ma, Ming; Lou, Zhiyong

2008-01-01

Human calbindin-D28k has been overexpressed in E. coli, purified and crystallized. Diffraction data were collected to 2.4 Å resolution. Calbindin-D28k is a calcium-binding protein that belongs to the troponin C superfamily. It is expressed in many tissues, including brain, intestine, kidney and pancreas, and performs roles as both a calcium buffer and a calcium sensor and carries out diverse physiological functions of importance. In order to resolve the crystal structure of human calbindin-D28k and to gain a better understanding of its biological functions, recombinant human calbindin-D28k was crystallized at 291 K using PEG 3350 as precipitant and a 2.4 Å resolution X-ray data set was collected from a single flash-cooled crystal (100 K). The crystal belonged to space group C2, with unit-cell parameters a = 108.1, b = 28.2, c = 70.6 Å, β = 107.8°. The presence of one molecule per asymmetric unit is presumed, corresponding to a Matthews coefficient of 1.75 Å 3 Da −1

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

Energy Technology Data Exchange (ETDEWEB)

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

2010-07-20

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

Crystal structure analysis, overexpression and refolding behaviour of a DING protein with single mutation

International Nuclear Information System (INIS)

Gai, Zuoqi; Nakamura, Akiyoshi; Tanaka, Yoshikazu; Hirano, Nagisa; Tanaka, Isao; Yao, Min

2013-01-01

Crystals of a member of the DING protein family (HPBP) were obtained accidentally, and the structure was determined at 1.35 Å resolution. For further analysis, a system for preparation of HPBP was constructed and the structure of a prepared sample was confirmed by X-ray crystal structure analysis at 1.03 Å resolution. After crystallization of a certain protein–RNA complex, well diffracting crystals were obtained. However, the asymmetric unit of the crystal was too small to locate any components. Mass spectrometry and X-ray crystal structure analysis showed that it was a member of the DING protein family (HPBP). Surprisingly, the structure of HPBP reported previously was also determined accidentally as a contaminant, suggesting that HPBP has a strong tendency to crystallize. Furthermore, DING proteins were reported to relate in disease. These observations suggest that DING has potential for application in a wide range of research fields. To enable further analyses, a system for preparation of HPBP was constructed. As HPBP was expressed in insoluble form in Escherichia coli, it was unfolded chemically and refolded. Finally, a very high yield preparation method was constructed, in which 43 mg of HPBP was obtained from 1 L of culture. Furthermore, to evaluate the validity of refolding, its crystal structure was determined at 1.03 Å resolution. The determined structure was identical to the native structure, in which two disulfide bonds were recovered correctly and a phosphate ion was captured. Based on these results, it was concluded that the refolded HPBP recovers its structure correctly

Crystal structure analysis, overexpression and refolding behaviour of a DING protein with single mutation

Energy Technology Data Exchange (ETDEWEB)

Gai, Zuoqi; Nakamura, Akiyoshi [Hokkaido University, Sapporo 060-0810 (Japan); Tanaka, Yoshikazu, E-mail: tanaka@sci.hokudai.ac.jp [Hokkaido University, Sapporo 060-0810 (Japan); Hokkaido University, Sapporo 060-0810 (Japan); Hirano, Nagisa [Hokkaido University, Sapporo 060-0810 (Japan); Tanaka, Isao; Yao, Min [Hokkaido University, Sapporo 060-0810 (Japan); Hokkaido University, Sapporo 060-0810 (Japan)

2013-11-01

Crystals of a member of the DING protein family (HPBP) were obtained accidentally, and the structure was determined at 1.35 Å resolution. For further analysis, a system for preparation of HPBP was constructed and the structure of a prepared sample was confirmed by X-ray crystal structure analysis at 1.03 Å resolution. After crystallization of a certain protein–RNA complex, well diffracting crystals were obtained. However, the asymmetric unit of the crystal was too small to locate any components. Mass spectrometry and X-ray crystal structure analysis showed that it was a member of the DING protein family (HPBP). Surprisingly, the structure of HPBP reported previously was also determined accidentally as a contaminant, suggesting that HPBP has a strong tendency to crystallize. Furthermore, DING proteins were reported to relate in disease. These observations suggest that DING has potential for application in a wide range of research fields. To enable further analyses, a system for preparation of HPBP was constructed. As HPBP was expressed in insoluble form in Escherichia coli, it was unfolded chemically and refolded. Finally, a very high yield preparation method was constructed, in which 43 mg of HPBP was obtained from 1 L of culture. Furthermore, to evaluate the validity of refolding, its crystal structure was determined at 1.03 Å resolution. The determined structure was identical to the native structure, in which two disulfide bonds were recovered correctly and a phosphate ion was captured. Based on these results, it was concluded that the refolded HPBP recovers its structure correctly.

Production, purification, crystallization and structure determination of H-1 Parvovirus

International Nuclear Information System (INIS)

Halder, Sujata; Nam, Hyun-Joo; Govindasamy, Lakshmanan; Vogel, Michèle; Dinsart, Christiane; Salomé, Nathalie; McKenna, Robert; Agbandje-McKenna, Mavis

2012-01-01

The production, purification, crystallization and crystallographic analysis of H-1 Parvovirus, a gene-therapy vector, are reported. Crystals of H-1 Parvovirus (H-1PV), an antitumor gene-delivery vector, were obtained for DNA-containing capsids and diffracted X-rays to 2.7 Å resolution using synchrotron radiation. The crystals belonged to the monoclinic space group P2 1 , with unit-cell parameters a = 255.4, b = 350.4, c = 271.6 Å, β = 90.34°. The unit cell contained two capsids, with one capsid per crystallographic asymmetric unit. The H-1PV structure has been determined by molecular replacement and is currently being refined

Purification, crystallization and preliminary crystallographic analysis of biotin protein ligase from Staphylococcus aureus.

Science.gov (United States)

Pendini, Nicole R; Polyak, Steve W; Booker, Grant W; Wallace, John C; Wilce, Matthew C J

2008-06-01

Biotin protein ligase from Staphylococcus aureus catalyses the biotinylation of acetyl-CoA carboxylase and pyruvate carboxylase. Recombinant biotin protein ligase from S. aureus has been cloned, expressed and purified. Crystals were grown using the hanging-drop vapour-diffusion method using PEG 8000 as the precipitant at 295 K. X-ray diffraction data were collected to 2.3 A resolution from crystals using synchrotron X-ray radiation at 100 K. The diffraction was consistent with the tetragonal space group P4(2)2(1)2, with unit-cell parameters a = b = 93.665, c = 131.95.

The accuracy of the crystal chemical parameters at high-pressure conditions from single-crystal X-ray diffraction in diamond-anvil cell

DEFF Research Database (Denmark)

Periotto, Benedetta

-ray instruments. At the same time, the high-pressure experiments have benefited by the strong improvements on the high-pressure devices, in particular the diamond-anvil cell (DAC). The aim of this research project is to assess the quality of the data obtained by means of the single-crystal X-ray diffraction...... technique through the study of different mineral phases. The procedure for setting up an experiment under high-pressure conditions, using a single crystal as sample held within a DAC, are presented here with all the details of the in situ measurements at high-pressure conditions. The research project...... started with a comparison between two different DACs, in order to define the capabilities of one of the most common types of pressure device, the ETH-type DAC. Application examples of data quality analysis have been conducted on pyroxenes (NaInSi2O6, orthoenstatite MgSiO3 and LiCrSi2O6), which...

Introducing uncertainty analysis of nucleation and crystal growth models in Process Analytical Technology (PAT) system design of crystallization processes

DEFF Research Database (Denmark)

Abdul Samad, Noor Asma Fazli Bin; Sin, Gürkan; Gernaey, Krist

2013-01-01

This paper presents the application of uncertainty and sensitivity analysis as part of a systematic modelbased process monitoring and control (PAT) system design framework for crystallization processes. For the uncertainty analysis, the Monte Carlo procedure is used to propagate input uncertainty...

Error analysis of the crystal orientations obtained by the dictionary approach to EBSD indexing.

Science.gov (United States)

Ram, Farangis; Wright, Stuart; Singh, Saransh; De Graef, Marc

2017-10-01

The efficacy of the dictionary approach to Electron Back-Scatter Diffraction (EBSD) indexing was evaluated through the analysis of the error in the retrieved crystal orientations. EBSPs simulated by the Callahan-De Graef forward model were used for this purpose. Patterns were noised, distorted, and binned prior to dictionary indexing. Patterns with a high level of noise, with optical distortions, and with a 25 × 25 pixel size, when the error in projection center was 0.7% of the pattern width and the error in specimen tilt was 0.8°, were indexed with a 0.8° mean error in orientation. The same patterns, but 60 × 60 pixel in size, were indexed by the standard 2D Hough transform based approach with almost the same orientation accuracy. Optimal detection parameters in the Hough space were obtained by minimizing the orientation error. It was shown that if the error in detector geometry can be reduced to 0.1% in projection center and 0.1° in specimen tilt, the dictionary approach can retrieve a crystal orientation with a 0.2° accuracy. Copyright © 2017 Elsevier B.V. All rights reserved.

Ion Density Analysis of Single-Stranded DNA in Liquid Crystal

Science.gov (United States)

Iwabata, Kazuki; Seki, Yasutaka; Toizumi, Ryota; Shimada, Yuki; Furue, Hirokazu; Sakaguchi, Kengo

2013-09-01

With the widespread use of liquid crystals (LCs) in liquid crystal displays, we have looked into the application of liquid crystals in biotechnology. The purpose of the study described here is to investigate the physical properties of DNA using LCs. Synthetic oligonucleotide molecules were dispersed in MLC6884, the sample injected into antiparallel cells, and the amount of mobile ions was measured. The LC cell doped with oligonucleotide molecules showed a sequence-dependent, specific correlation between oligonucleotide concentration and the amount of mobile ions in the LC cells. In the framework of the Stokes model and polyacrylamide gel electrophoresis (PAGE) analysis, we speculate that this result arises from the difference in ion mobility, which is caused by the shape of the oligonucleotide molecule in the LC.

Crystal-field energy level analysis for Nd{sup 3+} ions at the low symmetry C{sub 1} site in [Nd(hfa){sub 4}(H{sub 2}O)](N(C{sub 2}H{sub 5}){sub 4}) single crystals

Energy Technology Data Exchange (ETDEWEB)

Mech, Agnieszka; Gajek, Zbigniew [Institute of Low Temperature and Structure Research, Polish Academy Of Sciences, ulica Okolna 2, 54-422 Wroclaw (Poland); Karbowiak, Miroslaw [Faculty of Chemistry, University of Wroclaw, ulica F Joliot-Curie 14, 50-383 Wroclaw (Poland); Rudowicz, Czeslaw [Institute of Physics, Szczecin University of Technology, Aleja Piastow 17, 70-310 Szczecin (Poland)], E-mail: karb@wchuwr.pl

2008-09-24

Optical absorption measurements of Nd{sup 3+} ions in single crystals of [Nd(hfa){sub 4}(H{sub 2}O)](N(C{sub 2}H{sub 5}){sub 4}) (hfa = hexafluoroacetyloacetonate), denoted Nd(hfa) for short, have been carried out at 4.2 and 298 K. This compound crystallizes in the monoclinic system (space group P 2{sub 1}/n). Each Nd ion is coordinated to eight oxygen atoms that originate from the hexafluoroacetylacetonate ligands and one oxygen atom from the water molecule. A total of 85 experimental crystal-field (CF) energy levels arising from the Nd{sup 3+} (4f{sup 3}) electronic configuration were identified in the optical spectra and assigned. A three-step CF analysis was carried out in terms of a parametric Hamiltonian for the actual C{sub 1} symmetry at the Nd{sup 3+} ion sites. In the first step, a total of 27 CF parameters (CFPs) in the Wybourne notation B{sub kq}, admissible by group theory, were determined in a preliminary fitting constrained by the angular overlap model predictions. The resulting CFP set was reduced to 24 specific independent CFPs using appropriate standardization transformations. Optimizations of the second-rank CFPs and extended scanning of the parameter space were employed in the second step to improve reliability of the CFP sets, which is rather a difficult task in the case of no site symmetry. Finally, seven free-ion parameters and 24 CFPs were freely varied, yielding an rms deviation between the calculated energy levels and the 85 observed ones of 11.1 cm{sup -1}. Our approach also allows prediction of the energy levels of Nd{sup 3+} ions that are hidden in the spectral range overlapping with strong ligand absorption, which is essential for understanding the inter-ionic energy transfer. The orientation of the axis system associated with the fitted CF parameters w.r.t. the crystallographic axes is established. The procedure adopted in our calculations may be considered as a general framework for analysis of CF levels of lanthanide ions at low

Quality control on pre-serial Bridgman production of PbWO{sub 4} scintillating crystals by means of photoelasticity

Energy Technology Data Exchange (ETDEWEB)

Rinaldi, D., E-mail: d.rinaldi@univpm.i [Dipartimento di Fisica e Ingegneria dei Materiali e del Territorio, Universita Politecnica delle Marche, via Brecce Bianche, 60131 Ancona (Italy); INFN section of Perugia (Italy); Ciriaco, A. [Dipartimento di Fisica e Ingegneria dei Materiali e del Territorio, Universita' Politecnica delle Marche, via Brecce Bianche, 60131 Ancona (Italy); Lebeau, M. [CERN PH department, 1211 Geneva 23 (Switzerland); Paone, N. [Dipartimento di Meccanica, Universita' Politecnica delle Marche, via Brecce Bianche, 60131 Ancona (Italy)

2010-04-11

Residual internal stresses in PbWO{sub 4} (PWO) scintillating crystals grown by Bridgman method have been systematically studied. Residual stresses induced during growth play an important role in production yield. Cracking probability during mechanical processing as well as stable mechanical properties in finished crystal are closely related to internal stress levels. A regular production of good-quality crystals requires a fast and easy feed-back on growth parameters. Samples from a pre-serial production were analyzed in order to give the producer a quality feed-back for process optimization. By means of photoelasticity, we measured residual stress distribution in several sections along the growth axis and for typical positions in every section. The stress analysis revealed defects occurring during the crystallization process, attributed to dislocations, lattice disorientation and poly-crystallinity. This work had been prompted by the need for quality monitoring of a pre-serial production of PWO for the CMS experiment at CERN's LHC. Mapping stress levels inside the ingot volume and proposing a synthetic parameter to be used as a quality indicator, the resulting analysis should contribute to parameter optimization and improve the growth performance. The proposed method may be useful in conventional crystal production.

Cloning, purification, crystallization and preliminary crystallographic analysis of LsrR from Escherichia coli

International Nuclear Information System (INIS)

Liu, Xiaotian; Wu, Minhao; Sun, Demeng; Zang, Jianye

2010-01-01

The E. coli transcription repressor LsrR has been overexpressed, purified and crystallized. Diffraction data were collected to about 3 Å resolution. In Escherichia coli, the lsr operon is composed of six genes lsrACDBFG which regulate uptake and modification of the signalling molecule AI-2. LsrR is a repressor of the lsr operon and itself, which can bind phospho-AI-2 and be released from the promoter region of the operon and thus activate gene expression. LsrR fused with an HHHHHH sequence at the C-terminus was expressed, purified and crystallized in order to determine its structure and elucidate the molecular mechanism of repression. The crystal belonged to space group I222, with unit-cell parameters a = 79.84, b = 116.65, c = 186.04 Å, and was estimated to contain two protein molecules per asymmetric unit

Purification, crystallization and preliminary crystallographic analysis of Streptococcus pyogenes laminin-binding protein Lbp

International Nuclear Information System (INIS)

Linke, Christian; Caradoc-Davies, Tom T.; Proft, Thomas; Baker, Edward N.

2008-01-01

The S. pyogenes laminin-binding protein Lbp, which is essential for adhesion to human laminin, has been expressed, purified and crystallized. The laminin-binding protein Lbp (Spy2007) from Streptococcus pyogenes (a group A streptococcus) mediates adhesion to the human basal lamina glycoprotein laminin. Accordingly, Lbp is essential in in vitro models of cell adhesion and invasion. However, the molecular and structural basis of laminin binding by bacteria remains unknown. Therefore, the lbp gene has been cloned for recombinant expression in Escherichia coli. Lbp has been purified and crystallized from 30%(w/v) PEG 1500 by the sitting-drop vapour-diffusion method. The crystals belonged to the monoclinic space group P2 1 , with unit-cell parameters a = 42.62, b = 92.16, c = 70.61 Å, β = 106.27°, and diffracted to 2.5 Å resolution

Purification, crystallization and preliminary crystallographic analysis of Streptococcus pyogenes laminin-binding protein Lbp

Energy Technology Data Exchange (ETDEWEB)

Linke, Christian, E-mail: clin180@ec.auckland.ac.nz [School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland (New Zealand); Caradoc-Davies, Tom T. [School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland (New Zealand); Australian Synchrotron, Clayton, Victoria 3168 (Australia); Proft, Thomas [School of Medical Sciences, University of Auckland, Private Bag 92019, Auckland (New Zealand); Baker, Edward N. [School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland (New Zealand)

2008-02-01

The S. pyogenes laminin-binding protein Lbp, which is essential for adhesion to human laminin, has been expressed, purified and crystallized. The laminin-binding protein Lbp (Spy2007) from Streptococcus pyogenes (a group A streptococcus) mediates adhesion to the human basal lamina glycoprotein laminin. Accordingly, Lbp is essential in in vitro models of cell adhesion and invasion. However, the molecular and structural basis of laminin binding by bacteria remains unknown. Therefore, the lbp gene has been cloned for recombinant expression in Escherichia coli. Lbp has been purified and crystallized from 30%(w/v) PEG 1500 by the sitting-drop vapour-diffusion method. The crystals belonged to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 42.62, b = 92.16, c = 70.61 Å, β = 106.27°, and diffracted to 2.5 Å resolution.

Crystallization and preliminary X-ray diffraction analysis of Nsp15 from SARS coronavirus

International Nuclear Information System (INIS)

Ricagno, Stéfano; Coutard, Bruno; Grisel, Sacha; Brémond, Nicolas; Dalle, Karen; Tocque, Fabienne; Campanacci, Valérie; Lichière, Julie; Lantez, Violaine; Debarnot, Claire; Cambillau, Christian; Canard, Bruno; Egloff, Marie-Pierre

2006-01-01

Crystals of Nsp15 from the aetiological agent of SARS have been grown at room temperature. Crystals have cubic symmetry and diffract to a maximum resolution of 2.7 Å. The non-structural protein Nsp15 from the aetiological agent of SARS (severe acute respiratory syndrome) has recently been characterized as a uridine-specific endoribonuclease. This enzyme plays an essential role in viral replication and transcription since a mutation in the related H229E human coronavirus nsp15 gene can abolish viral RNA synthesis. SARS full-length Nsp15 (346 amino acids) has been cloned and expressed in Escherichia coli with an N-terminal hexahistidine tag and has been purified to homogeneity. The protein was subsequently crystallized using PEG 8000 or 10 000 as precipitants. Small cubic crystals of the apoenzyme were obtained from 100 nl nanodrops. They belong to space group P4 1 32 or P4 3 32, with unit-cell parameters a = b = c = 166.8 Å. Diffraction data were collected to a maximum resolution of 2.7 Å

Crystallization and preliminary diffraction analysis of a DsbA homologue from Wolbachia pipientis

Energy Technology Data Exchange (ETDEWEB)

Kurz, M. [Institute for Molecular Bioscience and ARC Special Research Centre for Functional and Applied Genomics, University of Queensland, St Lucia, QLD 4072 (Australia); Iturbe-Ormaetxe, I. [School of Integrative Biology, The University of Queensland, St Lucia, QLD 4072 (Australia); Jarrott, R. [Institute for Molecular Bioscience and ARC Special Research Centre for Functional and Applied Genomics, University of Queensland, St Lucia, QLD 4072 (Australia); O’Neill, S. L. [School of Integrative Biology, The University of Queensland, St Lucia, QLD 4072 (Australia); Byriel, K. A.; Martin, J. L., E-mail: j.martin@imb.uq.edu.au; Heras, B., E-mail: j.martin@imb.uq.edu.au [Institute for Molecular Bioscience and ARC Special Research Centre for Functional and Applied Genomics, University of Queensland, St Lucia, QLD 4072 (Australia)

2008-02-01

The first crystallization of a W. pipientis protein, α-DsbA1, was achieved using hanging-drop and sitting-drop vapour diffusion. α-DsbA1 is one of two DsbA homologues encoded by the Gram-negative α-proteobacterium Wolbachia pipientis, an endosymbiont that can behave as a reproductive parasite in insects and as a mutualist in medically important filarial nematodes. The α-DsbA1 protein is thought to be important for the folding and secretion of Wolbachia proteins involved in the induction of reproductive distortions. Crystals of native and SeMet α-DsbA1 were grown by vapour diffusion and belong to the monoclinic space group C2, with unit-cell parameters a = 71.4, b = 49.5, c = 69.3 Å, β = 107.0° and one molecule in the asymmetric unit (44% solvent content). X-ray data were recorded from native crystals to a resolution of 2.01 Å using a copper anode and data from SeMet α-DsbA1 crystals were recorded to 2.45 Å resolution using a chromium anode.

Crystallization and preliminary crystallographic analysis of poly(3-hydroxybutyrate) depolymerase from Bacillus thuringiensis.

Science.gov (United States)

Wang, Yung Lin; Lin, Yi Ting; Chen, Chia Lin; Shaw, Gwo Chyuan; Liaw, Shwu Huey

2014-10-01

Poly[(R)-3-hydroxybutyrate] (PHB) is a microbial biopolymer that has been commercialized as biodegradable plastics. The key enzyme for the degradation is PHB depolymerase (PhaZ). A new intracellular PhaZ from Bacillus thuringiensis (BtPhaZ) has been screened for potential applications in polymer biodegradation. Recombinant BtPhaZ was crystallized using 25% polyethylene glycol 3350, 0.2 M ammonium acetate, 0.1 M bis-tris pH 6.5 at 288 K. The crystals belonged to space group P1, with unit-cell parameters a = 42.97, b = 83.23, c = 85.50 Å, α = 73.45, β = 82.83, γ = 83.49°. An X-ray diffraction data set was collected to 1.42 Å resolution with an Rmerge of 6.4%. Unexpectedly, a molecular-replacement solution was obtained using the crystal structure of Streptomyces lividans chloroperoxidase as a template, which shares 24% sequence identity to BtPhaZ. This is the first crystal structure of an intracellular poly(3-hydroxybutyrate) depolymerase.

Crystallization and preliminary X-ray diffraction analysis of Nsp15 from SARS coronavirus

Energy Technology Data Exchange (ETDEWEB)

Ricagno, Stéfano; Coutard, Bruno; Grisel, Sacha; Brémond, Nicolas; Dalle, Karen; Tocque, Fabienne; Campanacci, Valérie; Lichière, Julie; Lantez, Violaine; Debarnot, Claire; Cambillau, Christian; Canard, Bruno; Egloff, Marie-Pierre, E-mail: marie-pierre.egloff@afmb.univ-mrs.fr [Centre National de la Recherche Scientifique and Universités d’Aix-Marseille I et II, UMR 6098, Architecture et Fonction des Macromolécules Biologiques, Ecole Supérieure d’Ingénieurs de Luminy-Case 925, 163 Avenue de Luminy, 13288 Marseille CEDEX 9 (France)

2006-04-01

Crystals of Nsp15 from the aetiological agent of SARS have been grown at room temperature. Crystals have cubic symmetry and diffract to a maximum resolution of 2.7 Å. The non-structural protein Nsp15 from the aetiological agent of SARS (severe acute respiratory syndrome) has recently been characterized as a uridine-specific endoribonuclease. This enzyme plays an essential role in viral replication and transcription since a mutation in the related H229E human coronavirus nsp15 gene can abolish viral RNA synthesis. SARS full-length Nsp15 (346 amino acids) has been cloned and expressed in Escherichia coli with an N-terminal hexahistidine tag and has been purified to homogeneity. The protein was subsequently crystallized using PEG 8000 or 10 000 as precipitants. Small cubic crystals of the apoenzyme were obtained from 100 nl nanodrops. They belong to space group P4{sub 1}32 or P4{sub 3}32, with unit-cell parameters a = b = c = 166.8 Å. Diffraction data were collected to a maximum resolution of 2.7 Å.

Theoretical study of the slow neutron coherent scattering by nemanic liquid crystals

International Nuclear Information System (INIS)

Sugakov, V.I.; Shiyanovskij, S.V.

1982-01-01

An exact expression is obtained for neutron coherent quasielastic scattering cross section in nematic liquid crystals. Expressions are analyzed or big and small values of scattering wave vector. In the first case scattering is occured on the separate molecules and the account of the molecule form noncylindricity is to be essential. In the second case an intermolecular correlations contribute greatly to cross sections. A connection is found for pair correlation function with fluctuation for density, dipole moment and order parameters. The performed cross section analysis allow to determine the significant microscopic parameters of the nematic liquid crystal from the experimental data of slow neutron scattering

Crystal growth and spectroscopic characterization of Yb3+:LiTaO3

International Nuclear Information System (INIS)

Gruber, John B.; Allik, Toomas H.; Sardar, Dhiraj K.; Yow, Raylon M.; Scripsick, Michael; Wechsler, Barry

2006-01-01

Spectroscopic properties are presented for Yb 3+ incorporated into single crystals of LiTaO 3 grown by the top-seeded solution growth method. From an analysis of the absorption and fluorescence spectra, we are able to determine the Stark-level components of the 2 F 7/2 (the ground-state multiplet manifold) and the 2 F 5/2 (the excited-state multiplet manifold of Yb 3+ (4f 13 )). The room-temperature fluorescence lifetime of 2 F 5/2 is 678μs as measured on a thin sample to reduce possibilities for reabsorption. Spectral comparisons of Yb 3+ -doped LiTaO 3 and LiNbO 3 are drawn. The crystal-field splitting of Yb 3+ (4f 13 ) in both crystal hosts is modeled using a set of crystal-field splitting parameters, B nm , determined from a recent spectroscopic analysis of Er 3+ (4f 11 ) in LiNbO 3 . Without adjustment of the B nm parameters, the model predicts the Stark-level energy and the symmetry label for each level in reasonable agreement with the experimental values. Less photorefractive than its niobate cousin, LiTaO 3 has potential for use in numerous integrated electro-optical circuits and devices

Maximizing Macromolecule Crystal Size for Neutron Diffraction Experiments

Science.gov (United States)

Judge, R. A.; Kephart, R.; Leardi, R.; Myles, D. A.; Snell, E. H.; vanderWoerd, M.; Curreri, Peter A. (Technical Monitor)

2002-01-01

A challenge in neutron diffraction experiments is growing large (greater than 1 cu mm) macromolecule crystals. In taking up this challenge we have used statistical experiment design techniques to quickly identify crystallization conditions under which the largest crystals grow. These techniques provide the maximum information for minimal experimental effort, allowing optimal screening of crystallization variables in a simple experimental matrix, using the minimum amount of sample. Analysis of the results quickly tells the investigator what conditions are the most important for the crystallization. These can then be used to maximize the crystallization results in terms of reducing crystal numbers and providing large crystals of suitable habit. We have used these techniques to grow large crystals of Glucose isomerase. Glucose isomerase is an industrial enzyme used extensively in the food industry for the conversion of glucose to fructose. The aim of this study is the elucidation of the enzymatic mechanism at the molecular level. The accurate determination of hydrogen positions, which is critical for this, is a requirement that neutron diffraction is uniquely suited for. Preliminary neutron diffraction experiments with these crystals conducted at the Institute Laue-Langevin (Grenoble, France) reveal diffraction to beyond 2.5 angstrom. Macromolecular crystal growth is a process involving many parameters, and statistical experimental design is naturally suited to this field. These techniques are sample independent and provide an experimental strategy to maximize crystal volume and habit for neutron diffraction studies.

On dewetting of thin films due to crystallization (crystallization dewetting).

Science.gov (United States)

Habibi, Mehran; Rahimzadeh, Amin; Eslamian, Morteza

2016-03-01

Drying and crystallization of a thin liquid film of an ionic or a similar solution can cause dewetting in the resulting thin solid film. This paper aims at investigating this type of dewetting, herein termed "crystallization dewetting", using PbI2 dissolved in organic solvents as the model solution. PbI2 solid films are usually used in X-ray detection and lead halide perovskite solar cells. In this work, PbI2 films are fabricated using spin coating and the effect of major parameters influencing the crystallization dewetting, including the type of the solvent, solution concentration, drying temperature, spin speed, as well as imposed vibration on the substrate are studied on dewetting, surface profile and coverage, using confocal scanning laser microscopy. Simplified hydrodynamic governing equations of crystallization in thin films are presented and using a mathematical representation of the process, it is phenomenologically demonstrated that crystallization dewetting occurs due to the absorption and consumption of the solution surrounding a growing crystal. Among the results, it is found that a low spin speed (high thickness), a high solution concentration and a low drying temperature promote crystal growth, and therefore crystallization dewetting. It is also shown that imposed vibration on the substrate can affect the crystal size and crystallization dewetting.

Quality inspection of anisotropic scintillating crystals through measurement of interferometric fringe pattern parameters

CERN Document Server

Cocozzella, N; Majni, G; Paone, N; Rinaldi, D T

2001-01-01

Scintillating crystals are widely used as detectors in radiographic systems, computerized axial tomography devices and in calorimeters employed in high-energy physics. This paper results from a project motivated by the development of the CMS calorimeter at CERN, which will make use of a large number of scintillating crystals. In order to prevent crystals from breaking because of internal residual stress, a quality control system based on optic inspection of interference fringe patterns was developed. The principle of measurement procedures was theoretically modelled, and then a dedicated polariscope was designed and built, in order to observe the crystals under induced stresses or to evaluate the residual internal stresses. The results are innovative and open a new perspective for scintillating crystals quality control: the photoelastic constant normal to the optic axis of the lead tungstate crystals (PbWO sub 4) was measured, and the inspection procedure developed is applicable to mass production, not only t...

Purification, crystallization and preliminary X-ray analysis of Enterococcus faecium aminoglycoside-2′′-phosphotransferase-Ib [APH(2′′)-Ib

Energy Technology Data Exchange (ETDEWEB)

Walanj, Rupa; Young, Paul; Baker, Heather M.; Baker, Edward N.; Metcalf, Peter [Laboratory of Structural Biology, School of Biological Sciences, University of Auckland, Auckland (New Zealand); Chow, Joseph W.; Lerner, Stephen [Division of Infectious Diseases, Wayne State University School of Medicine and VA Medical Center, Detroit, Michigan 48201 (United States); Vakulenko, Sergei [Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 (United States); Smith, Clyde A., E-mail: csmith@slac.stanford.edu [Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, CA 94025 (United States); Laboratory of Structural Biology, School of Biological Sciences, University of Auckland, Auckland (New Zealand)

2005-04-01

APH(2′′)-Ib is an enzyme responsible for high-level gentamicin resistance in E. faecium isolates. Native crystals of this enzyme have been prepared and preliminary X-ray diffraction experiments have been undertaken. Bacterial resistance to the aminoglycoside antibiotics is primarily the result of deactivation of the drugs. Three families of enzymes are responsible for this activity, with one such family being the aminoglycoside phosphotransferases (APHs). The gene encoding one of these enzymes, APH(2′′)-Ib, has been cloned and the protein (comprising 299 amino-acid residues) expressed in Escherichia coli, purified and crystallized in the presence of 16%(w/v) PEG 3350 and gentamicin. The crystals belong to the monoclinic space group P2{sub 1}, with approximate unit-cell parameters a = 79.7, b = 58.8, c = 81.4 Å, β = 98.4°, and preliminary X-ray diffraction analysis is consistent with the presence of two molecules in the asymmetric unit. Synchrotron diffraction data to approximately 2.65 Å resolution were collected from a native APH(2′′)-Ib crystal at beamline BL9-2 at SSRL (Stanford, CA, USA). Selenium-substituted crystals have also been produced and structure determination is proceeding.

Expression, crystallization and preliminary X-ray crystallographic analysis of human agmatinase

Energy Technology Data Exchange (ETDEWEB)

Kim, Kyoung Hoon; Ahn, Hyung Jun; Kim, Do Jin; Lee, Hyung Ho; Ha, Jun-Yong; Kim, Hye-Kyung; Yoon, Hye-Jin; Suh, Se Won, E-mail: sewonsuh@snu.ac.kr [Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742 (Korea, Republic of)

2005-10-01

Human agmatinase (Ala36–Val352) was overexpressed and crystallized, and X-ray diffraction data were collected to 2.49 Å. Agmatine, which results from the decarboxylation of l-arginine by arginine decarboxylase, is a metabolic intermediate in the biosynthesis of putresine and higher polyamines (spermidine and spermine). Recent studies indicate that agmatine can have several important biochemical effects in humans, ranging from effects on the central nervous system to cell proliferation in cancer and viral replication. Agmatinase catalyses the hydrolysis of agmatine to putresine and urea and is a major target for drug action and development. The human agmatinase gene encodes a 352-residue protein with a putative mitochondrial targeting sequence at the N-terminus. Human agmatinase (residues Ala36–Val352) has been overexpressed as a fusion with both N- and C-terminal purification tags in Escherichia coli and crystallized in the presence of Mn{sup 2+} and 1,6-diaminohexane at 297 K using polyethylene glycol 4000 as a precipitant. X-ray diffraction data were collected at 100 K to 2.49 Å from a flash-frozen crystal. The crystals are tetragonal, belonging to space group P4{sub 2}, with unit-cell parameters a = b = 114.54, c = 125.65 Å, α = β = γ = 90°. Three monomers are likely to be present in the asymmetric unit, giving a crystal volume per protein weight (V{sub M}) of 3.66 Å{sup 3} Da{sup −1} and a solvent content of 66.4%.

Transfiguring structural, optical and dielectric properties of cadmium thiourea acetate crystal by the addition of L-threonine for laser assisted device applications

Science.gov (United States)

Kulkarni, Rupali B.; Anis, Mohd; Hussaini, S. S.; Shirsat, Mahendra D.

2018-03-01

Present investigation reports the growth of pure and L-threonine (LT) doped cadmium thiourea acetate (CTA) crystals by slow solution evaporation technique followed by structural, optical and dielectric characterization studies. A bulk single crystal of LT-CTA has been grown at temperature 38 °C. The single crystal x-ray diffraction technique has been employed to confirm the structural parameters of pure and LT doped CTA crystals. The increase in optical transparency of LT-CTA crystal was ascertained in the range of 200 to 900 nm using UV-visible spectral analysis. The widened optical band gap of the LT-CTA crystal is found to be 4.7 eV. Pure and doped crystals are subjected to FT-IR analysis to indicate the presence of functional groups quantitatively. Appreciable enhancement in second harmonic generation (SHG) efficiency of LT-CTA crystal with reference to parent CTA was confirmed from Kurtz-Perry SHG test (1.31 times of CTA crystal). The assertive influence of LT on electrical properties of grown crystals has been investigated in the temperature range 35 °C-120 °C. Electronic purity and the color centered photoluminescence emission nature of pure and IA-CTA crystals were justified by luminescence analysis. With the aid of single beam Z-scan analysis, the Kerr lensing nonlinearity was identified and the magnitude of TONLO parameters has been determined. The cubic susceptibility (χ3) and figure of merit (FOM) was found to be 4.81 × 10-4esu and 978.35. Results vitalize LT-CTA for laser stabilization systems.

Statistical analysis of dynamic parameters of the core

International Nuclear Information System (INIS)

Ionov, V.S.

2007-01-01

The transients of various types were investigated for the cores of zero power critical facilities in RRC KI and NPP. Dynamic parameters of neutron transients were explored by tool statistical analysis. Its have sufficient duration, few channels for currents of chambers and reactivity and also some channels for technological parameters. On these values the inverse period. reactivity, lifetime of neutrons, reactivity coefficients and some effects of a reactivity are determinate, and on the values were restored values of measured dynamic parameters as result of the analysis. The mathematical means of statistical analysis were used: approximation(A), filtration (F), rejection (R), estimation of parameters of descriptive statistic (DSP), correlation performances (kk), regression analysis(KP), the prognosis (P), statistician criteria (SC). The calculation procedures were realized by computer language MATLAB. The reasons of methodical and statistical errors are submitted: inadequacy of model operation, precision neutron-physical parameters, features of registered processes, used mathematical model in reactivity meters, technique of processing for registered data etc. Examples of results of statistical analysis. Problems of validity of the methods used for definition and certification of values of statistical parameters and dynamic characteristics are considered (Authors)

Crystallization and preliminary crystallographic analysis of merohedrally twinned crystals of MJ0729, a CBS-domain protein from Methanococcus jannaschii

International Nuclear Information System (INIS)

Fernández-Millán, Pablo; Kortazar, Danel; Lucas, María; Martínez-Chantar, María Luz; Astigarraga, Egoitz; Fernández, José Andrés; Sabas, Olatz; Albert, Armando; Mato, Jose M.; Martínez-Cruz, Luis Alfonso

2008-01-01

Trigonal crystals of MJ0729 showing different degrees of merohedral twinning that may vary from perfect hemihedral twinning to perfect tetartohedral twinning were obtained upon slight variation of the pH. CBS domains are small protein motifs, usually associated in tandem, that are implicated in binding to adenosyl groups. Several genetic diseases in humans have been associated with mutations in CBS sequences, which has made them very promising targets for rational drug design. Trigonal crystals of the CBS-domain protein MJ0729 from Methanococcus jannaschii were grown by the vapour-diffusion method at acidic pH. Preliminary analysis of nine X-ray diffraction data sets using Yeates statistics and Britton plots showed that slight variation in the pH as well as in the buffer used in the crystallization experiments led to crystals with different degrees of merohedral twinning that may vary from perfect hemihedral twinning to perfect tetartohedral twinning

Integral data analysis for resonance parameters determination

International Nuclear Information System (INIS)

Larson, N.M.; Leal, L.C.; Derrien, H.

1997-09-01

Neutron time-of-flight experiments have long been used to determine resonance parameters. Those resonance parameters have then been used in calculations of integral quantities such as Maxwellian averages or resonance integrals, and results of those calculations in turn have been used as a criterion for acceptability of the resonance analysis. However, the calculations were inadequate because covariances on the parameter values were not included in the calculations. In this report an effort to correct for that deficiency is documented: (1) the R-matrix analysis code SAMMY has been modified to include integral quantities of importance, (2) directly within the resonance parameter analysis, and (3) to determine the best fit to both differential (microscopic) and integral (macroscopic) data simultaneously. This modification was implemented because it is expected to have an impact on the intermediate-energy range that is important for criticality safety applications

Expression, purification, crystallization and preliminary X-ray diffraction analysis of grass carp β2-microglobulin

International Nuclear Information System (INIS)

Chen, Weihong; Chu, Fuliang; Peng, Hao; Zhang, Jianhua; Qi, Jianxun; Jiang, Fan; Xia, Chun; Gao, Feng

2008-01-01

Grass carp β 2 -microglobulin was expressed in E. coli, purified to homogeneity and crystallized using the hanging-drop vapour-diffusion method with PEG 2K as precipitant. The crystals obtained belong to the orthorhombic space group P2 1 2 1 2 1 , with unit-cell parameters a = 38.72, b = 40.65, c = 71.12 Å. β 2 -Microglobulin (β 2 m) is an essential subunit of MHC I molecules; it stabilizes the structure of MHC I and plays a pivotal role in coreceptor recognition. To date, structures of β 2 m have been solved for three different mammals: human, mouse and cattle. In order to illuminate the molecular evolutionary origin of β2m, an understanding of its structure in lower vertebrates becomes important. Here, grass carp (Ctenopharyngodon idellus) β 2 m (Ctid-β 2 m) was expressed, purified and crystallized. Diffraction data were collected to a resolution of 2.5 Å. The crystal belongs to space group P2 1 2 1 2 1 , with unit-cell parameters a = 38.72, b = 40.65, c = 71.12 Å. The Matthews coefficient and the solvent content were calculated to be 2.56 Å Da −1 and 52.07%, respectively, for one molecule per asymmetric unit. The structure has been solved by molecular replacement using monomeric human β 2 m as a model

Human tRNAGly acceptor-stem microhelix: crystallization and preliminary X-ray diffraction analysis at 1.2 Å resolution

International Nuclear Information System (INIS)

Förster, Charlotte; Szkaradkiewicz, Karol; Perbandt, Markus; Brauer, Arnd B. E.; Borowski, Tordis; Fürste, Jens P.; Betzel, Christian; Erdmann, Volker A.

2007-01-01

The human tRNA Gly acceptor-stem microhelix was crystallized and preliminary X-ray diffraction analysis revealed diffraction to a resolution of up to 1.2 Å. The major dissimilarities between the eukaryotic/archaebacterial-type and eubacterial-type glycyl-tRNA synthetase systems (GlyRS; class II aminoacyl-tRNA synthetases) represent an intriguing example of evolutionarily divergent solutions to similar biological functions. The differences in the identity elements of the respective tRNA Gly systems are located within the acceptor stem and include the discriminator base U73. In the present work, the human tRNA Gly acceptor-stem microhelix was crystallized in an attempt to analyze the structural features that govern the correct recognition of tRNA Gly by the eukaryotic/archaebacterial-type glycyl-tRNA synthetase. The crystals of the human tRNA Gly acceptor-stem helix belong to the monoclinic space group C2, with unit-cell parameters a = 37.12, b = 37.49, c = 30.38 Å, α = γ = 90, β = 113.02°, and contain one molecule per asymmetric unit. A high-resolution data set was acquired using synchrotron radiation and the data were processed to 1.2 Å resolution

Quantitative analysis of thermal diffuse X-ray scattering on single crystals. Communication 2. FCC metals

International Nuclear Information System (INIS)

Najsh, V.E.; Novoselova, T.V.; Sagaradze, I.V.; Kvyatkovskij, B.E.; Fedorov, V.I.; Chernenkov, Yu.P.

1994-01-01

With the use of X-ray diffractometer a study was made into the intensity of diffuse scattering in Ni crystals with FCC lattice. Earlier accomplished quantitative analysis for BCC crystals was extended to FCC lattices. Comparative evaluation was made for cooperative thermal oscillation patterns and corresponding diffuse scattering in crystals of various structures. Measurements on FCC crystals were carried out at room temperature using AgK a lpha-radiation in 96 points of Ni crystal. 8 refs., 4 figs

Crystallization and preliminary X-ray analysis of an exotype alginate lyase Atu3025 from Agrobacterium tumefaciens strain C58, a member of polysaccharide lyase family 15

International Nuclear Information System (INIS)

Ochiai, Akihito; Yamasaki, Masayuki; Mikami, Bunzo; Hashimoto, Wataru; Murata, Kousaku

2006-01-01

The crystallization and preliminary X-ray characterization of a family PL-15 exotype alginate lyase are presented. Almost all alginate lyases depolymerize alginate in an endolytical fashion via a β-elimination reaction. The alginate lyase Atu3025 from Agrobacterium tumefaciens strain C58, consisting of 776 amino-acid residues, is a novel exotype alginate lyase classified into polysaccharide lyase family 15. The enzyme was crystallized at 293 K by sitting-drop vapour diffusion with polyethylene glycol 4000 as a precipitant. Preliminary X-ray analysis showed that the Atu3025 crystal belonged to space group P2 1 and diffracted to 2.8 Å resolution, with unit-cell parameters a = 107.7, b = 108.3, c = 149.5 Å, β = 91.5°

Investigations on the nucleation kinetics of γ-glycine single crystal

International Nuclear Information System (INIS)

Yogambal, C.; Rajan Babu, D.; Ezhil Vizhi, R.

2014-01-01

Single crystals of γ-glycine were grown by slow evaporation technique. The crystalline system was confirmed by single crystal X-ray diffraction analysis. The optical absorption study has shown that the grown crystal possesses lower cut-off wavelength. Solubility and metastable zone width were estimated for different temperatures. The induction period of title compound was determined by varying the temperature and concentration. Nucleation parameters such as Gibbs volume free energy change (ΔG v ), interfacial tension (γ), critical free energy change of the nucleus (ΔG ⁎ ), nucleation rate (J), number of molecules in the critical nucleus (i ⁎ ) have been calculated for the aqueous solution grown γ-glycine single crystals. The second harmonic generation (SHG) of γ-glycine was confirmed by Q-switched Nd:YAG laser technique

Crystallization and preliminary X-ray diffraction analysis of alanine racemase from Pseudomonas putida YZ-26

International Nuclear Information System (INIS)

Liu, Junlin; Feng, Lei; Shi, Yawei; Feng, Wei

2012-01-01

A recombinant alanine racemase from the Pseudomonas putida YZ-26, has been crystallized by the sitting-drop vapor-diffusion method and X-ray diffraction data were collected to 2.4 Å. A recombinant form of alanine racemase (Alr) from Pseudomonas putida YZ-26 has been crystallized by the sitting-drop vapour diffusion method. X-ray diffraction data were collected to 2.4 Å resolution. The crystals belong to the space group C222 1 , with unit-cell parameters a = 118.08, b = 141.86, c = 113.83 Å, and contain an Alr dimer in the asymmetric unit. The Matthews coefficient and the solvent content were calculated to be 2.8 Å 3 Da −1 and approximately 50%, respectively

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.

Phase transitions in A4Li(HSO4)3(SO4); A = Rb, K: Single crystal X ...

Indian Academy of Sciences (India)

Unknown

Single crystal studies on RLHS at room temperature (293 K) reported earlier5 showed that the crystals are optically laevorotatory and belong to the enantiomorphous space group P41. However, an analysis of the diffraction data based on the value of enantio- morph polarity parameter during refinement suggested that the ...

Cloning, overexpression, purification, crystallization and preliminary X-ray diffraction analysis of an inositol monophosphatase family protein (SAS2203) from Staphylococcus aureus MSSA476

International Nuclear Information System (INIS)

Bhattacharyya, Sudipta; Dutta, Debajyoti; Ghosh, Ananta Kumar; Das, Amit Kumar

2011-01-01

The cloning, overexpression, purification, crystallization and preliminary X-ray diffraction analysis of an inositol monophosphatase family protein (SAS2203) from S. aureus MSSA476 is reported. The gene product of the sas2203 ORF of Staphylococcus aureus MSSA476 encodes a 30 kDa molecular-weight protein with a high sequence resemblance (29% identity) to tetrameric inositol monophosphatase from Thermotoga maritima. The protein was cloned, expressed, purified to homogeneity and crystallized. Crystals appeared in several conditions and good diffraction-quality crystals were obtained from 0.2 M Li 2 SO 4 , 20% PEG 3350, 0.1 M HEPES pH 7.0 using the sitting-drop vapour-diffusion method. A complete diffraction data set was collected to 2.6 Å resolution using a Rigaku MicroMax-007 HF Cu Kα X-ray generator and a Rigaku R-AXIS IV ++ detector. The diffraction data were consistent with the orthorhombic space group P2 1 2 1 2 1 , with unit-cell parameters a = 49.98, b = 68.35, c = 143.79 Å, α = β = γ = 90°, and the crystal contained two molecules in the asymmetric unit

Thermal bump removal of a crystal monochromator by designing an optimal shape

Energy Technology Data Exchange (ETDEWEB)

Micha, Jean-Sébastien, E-mail: micha@esrf.fr [CRG-IF BM32 Beamline, ESRF, 6 rue J. Horowitz, BP 220, 38043 Grenoble (France); UMR SPrAM 5819, CEA-Grenoble/INAC/SPrAM, 17 avenue des Martyrs, 38054 Grenoble Cedex 9 (France); Geaymond, Olivier [CRG-IF BM32 Beamline, ESRF, 6 rue J. Horowitz, BP 220, 38043 Grenoble (France); Institut Néel, CNRS, 25 avenue des Martyrs, 38054 Grenoble Cedex 9 (France); Rieutord, Francois [CRG-IF BM32 Beamline, ESRF, 6 rue J. Horowitz, BP 220, 38043 Grenoble (France); CEA-Grenoble/INAC/NRS, 17 avenue des Martyrs, 38054 Grenoble Cedex 9 (France)

2013-05-11

Thermal bump arising at illuminated area of a water cooled monochromator crystal can be considerably reduced by designing an appropriate shape. Temperature and deformation have been simulated by finite element analysis (FEA) computations as a function of few geometrical parameters describing the shape of the crystal. As a result, a new crystal shape has been found which optimizes the throughput of a double crystals monochromator (DCM). Performances of the initial rectangular crystal and the new designed crystal predicted by FEA-based calculations and measured during experimental tests on a synchrotron beamline are reported. General design principles to overcome heat load issues and the objective function using the slope errors derived from FEA results are detailed. Current and foreseen performances at higher load are presented. Finally, advantages and limits of this simple-to-design and cheap solution are discussed.

Crystal growth, spectral and laser properties of Nd:LuAG single crystal

International Nuclear Information System (INIS)

Xu, X D; Meng, J Q; Cheng, Y; Li, D Z; Cheng, S S; Wu, F; Zhao, Z W; Wang, X D; Xu, J

2009-01-01

Nd:LuAG (Nd:Lu 3 Al 5 O 12 ) crystal was grown by the Czochralski method. X-ray powder diffraction experiments show that the Nd:LuAG crystal crystallizes in the cubic with space group Ia3d and has the cell parameter: a = 1.1907 nm, V = 1.6882 nm 3 . The absorption and fluorescence spectra of Nd:LuAG crystal at room temperature were investigated. With a fiber-coupled diode laser as pump source, the continuous-wave (CW) laser action of Nd:LuAG crystal was demonstrated. The maximum output power at 1064 nm was obtained to be 3.8 W under the incident pump power of 17.3 W, with the optical conversion efficiency 22.0% and the slope efficiency 25.7%

Crystal growth, spectral and laser properties of Nd:LuAG single crystal

Science.gov (United States)

Xu, X. D.; Wang, X. D.; Meng, J. Q.; Cheng, Y.; Li, D. Z.; Cheng, S. S.; Wu, F.; Zhao, Z. W.; Xu, J.

2009-09-01

Nd:LuAG (Nd:Lu3Al5O12) crystal was grown by the Czochralski method. X-ray powder diffraction experiments show that the Nd:LuAG crystal crystallizes in the cubic with space group Ia3d and has the cell parameter: a = 1.1907 nm, V = 1.6882 nm3. The absorption and fluorescence spectra of Nd:LuAG crystal at room temperature were investigated. With a fiber-coupled diode laser as pump source, the continuous-wave (CW) laser action of Nd:LuAG crystal was demonstrated. The maximum output power at 1064 nm was obtained to be 3.8 W under the incident pump power of 17.3 W, with the optical conversion efficiency 22.0% and the slope efficiency 25.7%.

Purification, crystallization and preliminary X-ray analysis of the IgV domain of human nectin-4

International Nuclear Information System (INIS)

Xu, Xiang; Zhang, Xiaoai; Lu, Guangwen; Cai, Yongping

2012-01-01

Nectin-4 belongs to a family of immunoglobulin-like cell adhesion molecules and is highly expressed in cancer cells. Recently, nectin-4 was found to be a receptor of measles virus and the IgV domain sustains strong binding to measles virus H protein. In this study, the successful expression and purification of human nectin-4 V domain (nectin-4v) is reported Nectin-4 belongs to a family of immunoglobulin-like cell adhesion molecules and is highly expressed in cancer cells. Recently, nectin-4 was found to be a receptor of measles virus and the IgV domain sustains strong binding to measles virus H protein. In this study, the successful expression and purification of human nectin-4 V domain (nectin-4v) is reported. The purified protein was crystallized using the sitting-drop vapour-diffusion method. The crystals diffracted to 1.8 Å resolution and belonged to space group P2 1 , with unit-cell parameters a = 33.1, b = 51.7, c = 56.9 Å, β = 94.7°. Preliminary analysis of the diffraction data was also performed

Crystallization and preliminary X-ray crystallographic analysis of BxlA, an intracellular β-d-xylosidase from Streptomyces thermoviolaceus OPC-520

International Nuclear Information System (INIS)

Morioka, Hideaki; Miki, Yasuhiro; Saito, Kei; Tomoo, Koji; Ishida, Toshimasa; Hasegawa, Tomokazu; Yamano, Akihito; Takada, Chiaki; Miyamoto, Katsushiro; Tsujibo, Hiroshi

2010-01-01

BxlA from Streptomyces thermoviolaceus OPC-520 (molecular weight 82 kDa) was crystallized by the hanging-drop vapour-diffusion method at 289 K. BxlA from Streptomyces thermoviolaceus OPC-520, together with the extracellular BxlE and the integral membrane proteins BxlF and BxlG, constitutes a xylanolytic system that participates in the intracellular transport of xylan-degradation products and the production of xylose. To elucidate the mechanism of the hydrolytic degradation of xylooligosaccharides to xylose at the atomic level, X-ray structural analysis of BxlA was attempted. The recombinant BxlA protein (molecular weight 82 kDa) was crystallized by the hanging-drop vapour-diffusion method at 289 K. The crystals belonged to the monoclinic space group C2, with unit-cell parameters a = 142.2, b = 129.5, c = 101.4 Å, β = 119.8°, and contained two molecules per asymmetric unit (V M = 2.47 Å 3 Da −1 ). Diffraction data were collected to a resolution to 2.50 Å and provided a data set with an overall R merge of 8.3%

Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations

International Nuclear Information System (INIS)

Streek, Jacco van de; Neumann, Marcus A.

2010-01-01

The accuracy of a dispersion-corrected density functional theory method is validated against 241 experimental organic crystal structures from Acta Cryst. Section E. This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095 Å (0.084 Å for the 225 ordered structures). R.m.s. Cartesian displacements above 0.25 Å either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect

Solid-state reaction kinetics and optical studies of cadmium doped magnesium hydrogen phosphate crystals

Science.gov (United States)

Verma, Madhu; Gupta, Rashmi; Singh, Harjinder; Bamzai, K. K.

2018-04-01

The growth of cadmium doped magnesium hydrogen phosphate was successfully carried out by using room temperature solution technique i.e., gel encapsulation technique. Grown crystals were confirmed by single crystal X-ray diffraction (XRD). The structure of the grown crystal belongs to orthorhombic crystal system and crystallizes in centrosymmetric space group. Kinetics of the decomposition of the grown crystals were studied by non-isothermal analysis. Thermo gravimetric / differential thermo analytical (TG/DTA) studies revealed that the grown crystal is stable upto 119 °C. The various steps involved in the thermal decomposition of the material have been analysed using Horowitz-Metzger, Coats-Redfern and Piloyan-Novikova equations for evaluating various kinetic parameters. The optical studies shows that the grown crystals possess wide transmittance in the visible region and significant optical band gap of 5.5ev with cut off wavelength of 260 nm.

Expression, purification, crystallization and preliminary crystallographic analysis of human Pim-1 kinase

International Nuclear Information System (INIS)

Qian, Kevin C.; Studts, Joey; Wang, Lian; Barringer, Kevin; Kronkaitis, Anthony; Peng, Charline; Baptiste, Alistair; LaFrance, Roger; Mische, Sheenah; Farmer, Bennett

2004-01-01

Pim kinases, belong to a distinctive serine/threonine protein-kinase family and are involved in cytokine-induced signal transduction and the development of lymphoid malignancies. Human Pim-1 kinase has been cloned, expressed and crystallized Pim kinases, including Pim-1, Pim-2 and Pim-3, belong to a distinctive serine/threonine protein-kinase family. They are involved in cytokine-induced signal transduction and the development of lymphoid malignancies. Their kinase domains are highly homologous to one another, but share low sequence identity to other kinases. Specifically, there are two proline residues in the conserved hinge-region sequence ERPXPX separated by a residue that is non-conserved among Pim kinases. Full-length human Pim-1 kinase (1–313) was cloned and expressed in Escherichia coli as a GST-fusion protein and truncated to Pim-1 (14–313) by thrombin digestion during purification. The Pim-1 (14–313) protein was purified to high homogeneity and monodispersity. This protein preparation yielded small crystals in the initial screening and large crystals after optimization. The large crystals of apo Pim-1 enzyme diffracted to 2.1 Å resolution and belong to space group P6 5 , with unit-cell parameters a = b = 95.9, c = 80.0 Å, β = 120° and one molecule per asymmetric unit

crystal

Science.gov (United States)

Yu, Yi; Huang, Yisheng; Zhang, Lizhen; Lin, Zhoubin; Sun, Shijia; Wang, Guofu

2014-07-01

A Nd3+:Na2La4(WO4)7 crystal with dimensions of ϕ 17 × 30 mm3 was grown by the Czochralski method. The thermal expansion coefficients of Nd3+:Na2La4(WO4)7 crystal are 1.32 × 10-5 K-1 along c-axis and 1.23 × 10-5 K-1 along a-axis, respectively. The spectroscopic characteristics of Nd3+:Na2La4(WO4)7 crystal were investigated. The Judd-Ofelt theory was applied to calculate the spectral parameters. The absorption cross sections at 805 nm are 2.17 × 10-20 cm2 with a full width at half maximum (FWHM) of 15 nm for π-polarization, and 2.29 × 10-20 cm2 with a FWHM of 14 nm for σ-polarization. The emission cross sections are 3.19 × 10-20 cm2 for σ-polarization and 2.67 × 10-20 cm2 for π-polarization at 1,064 nm. The fluorescence quantum efficiency is 67 %. The quasi-cw laser of Nd3+:Na2La4(WO4)7 crystal was performed. The maximum output power is 80 mW. The slope efficiency is 7.12 %. The results suggest Nd3+:Na2La4(WO4)7 crystal as a promising laser crystal fit for laser diode pumping.

Crystal growth and optical properties of Sm:CaNb2O6 single crystal

International Nuclear Information System (INIS)

Di Juqing; Xu Xiaodong; Xia Changtai; Zeng Huidan; Cheng Yan; Li Dongzhen; Zhou Dahua; Wu Feng; Cheng Jimeng; Xu Jun

2012-01-01

Highlights: ► Sm:CaNb 2 O 6 single crystal was grown by the Czochralski method. ► Thermal expansion coefficients and J–O parameters were calculated. ► We found that this crystal had high quantum efficiency of 97%. - Abstract: Sm:CaNb 2 O 6 single crystal has been grown by the Czochralski method. Its high-temperature X-ray powder diffraction, optical absorption, emission spectroscopic as well as lifetime have been studied. Thermal expansion coefficients (α), J–O parameters (Ω i ), radiative lifetime (τ rad ), branching ratios (β) and stimulated emission cross-sections (σ e ) were calculated. The quantum efficiency (η) was calculated to be 97%. The intense peak emission cross section at 610, 658 nm were calculated to be 2.40 × 10 −21 , 2.42 × 10 −21 cm 2 . These results indicate that Sm:CaNb 2 O 6 crystal has potential use in visible laser and photonic devices area.

Computerized analysis of brain perfusion parameter images

International Nuclear Information System (INIS)

Turowski, B.; Haenggi, D.; Wittsack, H.J.; Beck, A.; Aurich, V.

2007-01-01

Purpose: The development of a computerized method which allows a direct quantitative comparison of perfusion parameters. The display should allow a clear direct comparison of brain perfusion parameters in different vascular territories and over the course of time. The analysis is intended to be the basis for further evaluation of cerebral vasospasm after subarachnoid hemorrhage (SAH). The method should permit early diagnosis of cerebral vasospasm. Materials and Methods: The Angiotux 2D-ECCET software was developed with a close cooperation between computer scientists and clinicians. Starting from parameter images of brain perfusion, the cortex was marked, segmented and assigned to definite vascular territories. The underlying values were averages for each segment and were displayed in a graph. If a follow-up was available, the mean values of the perfusion parameters were displayed in relation to time. The method was developed under consideration of CT perfusion values but is applicable for other methods of perfusion imaging. Results: Computerized analysis of brain perfusion parameter images allows an immediate comparison of these parameters and follow-up of mean values in a clear and concise manner. Values are related to definite vascular territories. The tabular output facilitates further statistic evaluations. The computerized analysis is precisely reproducible, i. e., repetitions result in exactly the same output. (orig.)

Purification, crystallization and preliminary crystallographic analysis of histone lysine demethylase NO66 from Homo sapiens

International Nuclear Information System (INIS)

Zhou, Xing; Tao, Yue; Wu, Minhao; Zhang, Dandan; Zang, Jianye

2012-01-01

The JmjC domain-containing histone demethylase NO66 from H. sapiens was overproduced in E. coli, purified and crystallized. Diffraction data were collected to 2.29 Å resolution. NO66 is a JmjC domain-containing histone demethylase with specificity towards histone H3 methylated on both Lys4 and Lys36 in vitro and in vivo. A fragment of NO66 lacking the N-terminal 167 amino-acid residues was overexpressed in Escherichia coli, purified and crystallized using the sitting-drop vapour-diffusion method. X-ray diffraction data were collected to a resolution of 2.29 Å. NO66 crystallized in space group P3 1 or P3 2 , with unit-cell parameters a = 89.35, b = 89.35, c = 304.86 Å, α = β = 90, γ = 120°, and the crystal is likely to contain four molecules in the asymmetric unit

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

International Nuclear Information System (INIS)

MacElrevey, Celeste; Wedekind, Joseph E.

2005-01-01

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 1 2 1 2 or P4 3 2 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

Infrared dispersion analysis and Raman scattering spectra of taurine single crystals

Science.gov (United States)

Moreira, Roberto L.; Lobo, Ricardo P. S. M.; Dias, Anderson

2018-01-01

A comprehensive set of optical vibrational modes of monoclinic taurine crystals was determined by Raman scattering, and infrared reflectivity and transmission spectroscopies. By using appropriate scattering/reflection geometries, the vibrational modes were resolved by polarization and the most relevant modes of the crystal could be assigned. In particular, we were able to review the symmetry of the gerade modes and to resolve ambiguities in the literature. Owing to the non-orthogonal character of Bu modes in monoclinic crystals (lying on the optic axial plane), we carried out a generalized Lorentz dispersion analysis consisting of simultaneous adjust of infrared-reflectivity spectra at various light polarization angles. The Au modes (parallel to the C2-axis) were treated within the classical Lorentz model. The behavior of off-diagonal and diagonal terms of the complex dielectric tensors and the presence of anomalous dispersion were discussed as consequences of the low symmetry of the crystal.

Expression, purification, crystallization and preliminary X-ray diffraction analysis of Thermotoga neapolitana β-glucosidase B

Energy Technology Data Exchange (ETDEWEB)

Turner, Pernilla [Department of Biotechnology, Centre for Chemistry and Chemical Engineering, Lund University, Box 124, S-221 00 Lund (Sweden); Pramhed, Anna [Department of Molecular Biophysics, Centre for Chemistry and Chemical Engineering, Lund University, Box 124, S-221 00 Lund (Sweden); Kanders, Erik; Hedström, Martin; Karlsson, Eva Nordberg, E-mail: eva.nordberg-karlsson@biotek.lu.se [Department of Biotechnology, Centre for Chemistry and Chemical Engineering, Lund University, Box 124, S-221 00 Lund (Sweden); Logan, Derek T., E-mail: eva.nordberg-karlsson@biotek.lu.se [Department of Molecular Biophysics, Centre for Chemistry and Chemical Engineering, Lund University, Box 124, S-221 00 Lund (Sweden); Department of Biotechnology, Centre for Chemistry and Chemical Engineering, Lund University, Box 124, S-221 00 Lund (Sweden)

2007-09-01

Here, the expression, purification, crystallization and X-ray diffraction data of a family 3 β-glucosidase from the hyperthermophilic bacterium Thermotoga neapolitana are reported. β-Glucosidases belong to families 1, 3 and 9 of the glycoside hydrolases and act on cello-oligosaccharides. Family 1 and 3 enzymes are retaining and are reported to have transglycosylation activity, which can be used to produce oligosaccharides and glycoconjugates. Family 3 enzymes are less well characterized than their family 1 homologues and to date only two crystal structures have been solved. Here, the expression, purification, crystallization and X-ray diffraction data of a family 3 β-glucosidase from the hyperthermophilic bacterium Thermotoga neapolitana are reported. Crystals of selenomethionine-substituted protein have also been grown. The crystals belong to space group C222{sub 1}, with unit-cell parameters a = 74.9, b = 127.0, c = 175.2 Å. Native data have been collected to 2.4 Å resolution and the structure has been solved to 2.7 Å using the selenomethionine MAD method. Model building and refinement of the structure are under way.

Crystallization and preliminary crystallographic analysis of human Ca{sup 2+}-loaded calbindin-D28k

Energy Technology Data Exchange (ETDEWEB)

Zhang, Chang [Tsinghua-Nankai-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing 100084 (China); Sun, Yuna [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101 (China); Wang, Wei; Zhang, Yan [Tsinghua-Nankai-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing 100084 (China); Ma, Ming [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101 (China); Lou, Zhiyong, E-mail: louzy@xtal.tsinghua.edu.cn [Tsinghua-Nankai-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing 100084 (China)

2008-02-01

Human calbindin-D28k has been overexpressed in E. coli, purified and crystallized. Diffraction data were collected to 2.4 Å resolution. Calbindin-D28k is a calcium-binding protein that belongs to the troponin C superfamily. It is expressed in many tissues, including brain, intestine, kidney and pancreas, and performs roles as both a calcium buffer and a calcium sensor and carries out diverse physiological functions of importance. In order to resolve the crystal structure of human calbindin-D28k and to gain a better understanding of its biological functions, recombinant human calbindin-D28k was crystallized at 291 K using PEG 3350 as precipitant and a 2.4 Å resolution X-ray data set was collected from a single flash-cooled crystal (100 K). The crystal belonged to space group C2, with unit-cell parameters a = 108.1, b = 28.2, c = 70.6 Å, β = 107.8°. The presence of one molecule per asymmetric unit is presumed, corresponding to a Matthews coefficient of 1.75 Å{sup 3} Da{sup −1}.

Expression, purification, crystallization and preliminary X-ray diffraction analysis of Arabidopsis thaliana cyclophilin 38 (AtCyp38)

International Nuclear Information System (INIS)

Vasudevan, Dileep; Gopalan, Gayathri; He, Zengyong; Luan, Sheng; Swaminathan, Kunchithapadam

2005-01-01

Crystallization of Arabidopsis thaliana cyclophilin 38. The crystal diffracts X-rays to 2.5 Å resolution. AtCyp38 is one of the highly divergent multidomain cyclophilins from Arabidopsis thaliana. A recombinant form of AtCyp38 (residues 83–437) was expressed in Escherichia coli and purified to homogeneity. The protein was crystallized using the vapour-batch technique with PEG 6000 and t-butanol as precipitants. Crystals of recombinant AtCyp38 diffracted X-rays to better than 2.5 Å resolution at 95 K using a synchrotron-radiation source. The crystal belongs to the C-centred orthorhombic space group C222 1 , with unit-cell parameters a = 58.2, b = 95.9, c = 167.5 Å, and contains one molecule in the asymmetric unit. The selenomethionine derivative of the AtCyp38 protein was overexpressed, purified and crystallized in the same space group and data were collected to 3.5 Å at the NSLS synchrotron. The structure is being solved by the MAD method

Synthesis and crystal structure analysis of uranyl triple acetates

Energy Technology Data Exchange (ETDEWEB)

Klepov, Vladislav V., E-mail: vladislavklepov@gmail.com [Institute for Energy and Climate Research (IEK-6), Forschungszentrum Jülich GmbH, 52428 Jülich (Germany); Department of Chemistry, Samara National Research University, 443086 Samara (Russian Federation); Serezhkina, Larisa B.; Serezhkin, Victor N. [Department of Chemistry, Samara National Research University, 443086 Samara (Russian Federation); Alekseev, Evgeny V., E-mail: e.alekseev@fz-juelich.de [Institute for Energy and Climate Research (IEK-6), Forschungszentrum Jülich GmbH, 52428 Jülich (Germany); Institut für Kristallographie, RWTH Aachen University, 52066 Aachen (Germany)

2016-12-15

Single crystals of triple acetates NaR[UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 3}·6H{sub 2}O (R=Mg, Co, Ni, Zn), well-known for their use as reagents for sodium determination, were grown from aqueous solutions and their structural and spectroscopic properties were studied. Crystal structures of the mentioned phases are based upon (Na[UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 3}){sup 2–} clusters and [R(H{sub 2}O){sub 6}]{sup 2+} aqua-complexes. The cooling of a single crystal of NaMg[UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 3}·6H{sub 2}O from 300 to 100 K leads to a phase transition from trigonal to monoclinic crystal system. Intermolecular interactions between the structural units and their mutual packing were studied and compared from the point of view of the stereoatomic model of crystal structures based on Voronoi-Dirichlet tessellation. Using this method we compared the crystal structures of the triple acetates with Na[UO{sub 2}(CH{sub 3}COO){sub 3}] and [R(H{sub 2}O){sub 6}][UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 2} and proposed reasons of triple acetates stability. Infrared and Raman spectra were collected and their bands were assigned. - Graphical abstract: Single crystals of uranium based triple acetates, analytical reagents for sodium determination, were synthesized and structurally, spectroscopically and topologically characterized. The structures were compared with the structures of compounds from preceding families [M(H{sub 2}O){sub 6})][UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 2} (M = Mg, Co, Ni, Zn) and Na[UO{sub 2}(CH{sub 3}COO){sub 3}]. Analysis was performed with the method of molecular Voronoi-Dirichlet polyhedra to reveal a large contribution of the hydrogen bonds into intermolecular interactions which can be a reason of low solubility of studied complexes.

Hydrothermal Synthesis of Zeolitic Imidazolate Frameworks-8 (ZIF-8) Crystals with Controllable Size and Morphology

KAUST Repository

Lestari, Gabriella

2012-05-01

Zeolitic imidazolate frameworks (ZIFs) is a new class of metal-organic frameworks (MOFs) with zeolite-like properties such as permanent porosity, uniform pore size, and exceptional thermal and chemical stability. Until recently, ZIF materials have been mostly synthesized by solvothermal method. In this thesis, further analysis to tune the size and morphology of ZIF-8 is done upon our group’s recent success in preparing ZIF-8 crystals in pure aqueous solutions. Compositional parameters (molar ratio of 2-methylimidazole/Zn2+, type of zinc salt reagents, reagent concentrations, addition of surfactants) as well as process parameters (temperature and time) were systematically investigated. Upon characterizations of as-synthesized samples by X-ray powder diffraction, thermal gravimetric analysis, N2 adsorption, and field-emission scanning electron microscope, the results show that the particle size and morphology of ZIF-8 crystals are extremely sensitive to the compotional parameters of reagent concentration and addition of surfactants. The particle size and morphology of hydrothermally synthesized ZIF-8 crystals can be finely tuned; with the size ranging from 90 nm to 4 μm and the shape from truncated cubic to rhombic dodecahedron.

Crystallization and preliminary X-ray analysis of a novel Kunitz-type kallikrein inhibitor from Bauhinia bauhinioides

Science.gov (United States)

Navarro, Marcos Vicente de A. S.; Vierira, Débora F.; Nagem, Ronaldo A. P.; de Araújo, Ana Paula U.; Oliva, Maria Luiza V.; Garratt, Richard C.

2005-01-01

A Kunitz-type protease inhibitor (BbKI) found in Bauhinia bauhinioides seeds has been overexpressed in Escherichia coli and crystallized at 293 K using PEG 4000 as the precipitant. X-ray diffraction data have been collected to 1.87 Å resolution using an in-house X-ray generator. The crystals of the recombinant protein (rBbKI) belong to the orthorhombic space group P212121, with unit-cell parameters a = 46.70, b = 64.14, c = 59.24 Å. Calculation of the Matthews coefficient suggests the presence of one monomer of rBbKI in the asymmetric unit, with a corresponding solvent content of 51% (V M = 2.5 Å3 Da−1). Iodinated crystals were prepared and a derivative data set was also collected at 2.1 Å resolution. Crystals soaked for a few seconds in a cryogenic solution containing 0.5 M NaI were found to be reasonably isomorphous to the native crystals. Furthermore, the presence of iodide anions could be confirmed in the NaI-derivatized crystal. Data sets from native and derivative crystals are being evaluated for use in crystal structure determination by means of the SIRAS (single isomorphous replacement with anomalous scattering) method. PMID:16511193

Crystal growth and characterization of new semiorganic nonlinear optical single crystals

Energy Technology Data Exchange (ETDEWEB)

Kulshrestha, Shobha, E-mail: shobha011986@gmail.com; Shrivastava, A. K., E-mail: ashwaniaks@rediffmail.com [School of Studies in Physics, Jiwaji University Gwalior (M.P.) – 474 011 (India)

2016-05-06

An organic material of a L-histidine monohydrochloride single crystal was grown in a distilled water solution using the slow evaporation method at 40–45°C. The grown crystal was transparent and colourless, with a size of about 20 × 9 × 5 mm{sup 3}, obtained within a period of 21 days. The solubility of grown crystals have found out at various temperatures. The UV-visible transmittance studies show that the grown crystals have wide optical transparency in the entire visible region It is observed that the crystal has transparency window from 255nm to 700nm and its energy gap (Eg) found to be is 3.1eV. The grown crystal was subjected to powder X-ray diffraction analysis, confirming that the orthorhombic crystalline nature of the crystal. To identify the surface morphology, the as grown crystal was subjected to FE-SEM technique. The chemical composition of the grown crystal was estimated by Energy dispersive X-ray analysis. The optical behaviour of the grown crystal was analyzed by PL study.

Crystallization and preliminary X-ray analysis of a novel esterase Rv0045c from Mycobacterium tuberculosis

International Nuclear Information System (INIS)

Xu, Lipeng; Guo, Jiubiao; Zheng, Xiangdong; Wen, Tingyi; Sun, Fei; Liu, Siguo; Pang, Hai

2010-01-01

The novel esterase Rv0045c from M. tuberculosis was expressed and purified to homogeneity. The crystals of native and SeMet-labelled Rv0045c protein that were obtained diffracted to resolutions of 2.7 and 3.0 Å, respectively. The Rv0045c protein is predicted to be an esterase that is involved in lipid metabolism in Mycobacterium tuberculosis. The protein was overproduced in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. The Rv0045c protein crystals diffracted to a resolution of 2.7 Å using a synchrotron-radiation source and belonged to space group P3 1 or P3 2 , with unit-cell parameters a = b = 73.465, c = 48.064 Å, α = β = 90, γ = 120°. Purified SeMet-labelled Rv0045c protein was also crystallized and formed crystals that diffracted to a resolution of 3.0 Å using an in-house X-ray radiation source

Crystallization and preliminary X-ray diffraction analysis of the metalloregulatory protein DtxR from Thermoplasma acidophilum

International Nuclear Information System (INIS)

Yeo, Hyun Ku; Kang, Jina; Park, Young Woo; Sung, Jung-Suk; Lee, Jae Young

2012-01-01

Orthorhombic crystals of DtxR from T. acidophilum have been obtained. X-ray data were collected to 1.8 Å resolution using synchrotron radiation. The diphtheria toxin repressor (DtxR) is a metal-ion-dependent transcriptional regulator which regulates genes encoding proteins involved in metal-ion uptake to maintain metal-ion homeostasis. DtxR from Thermoplasma acidophilum was cloned and overexpressed in Escherichia coli. Crystals of N-terminally His-tagged DtxR were obtained by hanging-drop vapour diffusion and diffracted to 1.8 Å resolution. DtxR was crystallized at 296 K using polyethylene glycol 4000 as a precipitant. The crystals belonged to the orthorhombic space group P2 1 2 1 2, with unit-cell parameters a = 61.14, b = 84.61, c = 46.91 Å, α = β = γ = 90°. The asymmetric unit contained approximately one monomer of DtxR, giving a crystal volume per mass (V M ) of 2.22 Å 3 Da −1 and a solvent content of 44.6%

High-quality bulk hybrid perovskite single crystals within minutes by inverse temperature crystallization

KAUST Repository

Saidaminov, Makhsud I.

2015-07-06

Single crystals of methylammonium lead trihalide perovskites (MAPbX3; MA=CH3NH3+, X=Br− or I−) have shown remarkably low trap density and charge transport properties; however, growth of such high-quality semiconductors is a time-consuming process. Here we present a rapid crystal growth process to obtain MAPbX3 single crystals, an order of magnitude faster than previous reports. The process is based on our observation of the substantial decrease of MAPbX3 solubility, in certain solvents, at elevated temperatures. The crystals can be both size- and shape-controlled by manipulating the different crystallization parameters. Despite the rapidity of the method, the grown crystals exhibit transport properties and trap densities comparable to the highest quality MAPbX3 reported to date. The phenomenon of inverse or retrograde solubility and its correlated inverse temperature crystallization strategy present a major step forward for advancing the field on perovskite crystallization.

Crystallization and preliminary X-ray analysis of a novel Kunitz-type kallikrein inhibitor from Bauhinia bauhinioides

International Nuclear Information System (INIS)

Navarro, Marcos Vicente de A. S.; Vierira, Débora F.; Nagem, Ronaldo A. P.; Araújo, Ana Paula U. de; Oliva, Maria Luiza V.; Garratt, Richard C.

2005-01-01

Crystallization and preliminary X-ray diffraction studies are reported for a novel Kunitz-type protease inhibitor from B. bauhinioides which contains no disulfide bridges. A Kunitz-type protease inhibitor (BbKI) found in Bauhinia bauhinioides seeds has been overexpressed in Escherichia coli and crystallized at 293 K using PEG 4000 as the precipitant. X-ray diffraction data have been collected to 1.87 Å resolution using an in-house X-ray generator. The crystals of the recombinant protein (rBbKI) belong to the orthorhombic space group P2 1 2 1 2 1 , with unit-cell parameters a = 46.70, b = 64.14, c = 59.24 Å. Calculation of the Matthews coefficient suggests the presence of one monomer of rBbKI in the asymmetric unit, with a corresponding solvent content of 51% (V M = 2.5 Å 3 Da −1 ). Iodinated crystals were prepared and a derivative data set was also collected at 2.1 Å resolution. Crystals soaked for a few seconds in a cryogenic solution containing 0.5 M NaI were found to be reasonably isomorphous to the native crystals. Furthermore, the presence of iodide anions could be confirmed in the NaI-derivatized crystal. Data sets from native and derivative crystals are being evaluated for use in crystal structure determination by means of the SIRAS (single isomorphous replacement with anomalous scattering) method

Crystallization and preliminary X-ray crystallographic analysis of human PACSIN 1 protein

International Nuclear Information System (INIS)

Bai, Xiaoyun; Meng, Geng; Li, Guoming; Luo, Ming; Zheng, Xiaofeng

2009-01-01

A C-terminal truncation construct of human PACSIN 1 (1–344) has been purified and crystallized. Diffraction data were collected to 3.0 Å resolution. PACSIN 1, which is mainly detected in brain tissue, is one of the PACSIN-family proteins involved in endocytosis and recruitment of synaptic vesicles. It binds to dynamin, synaptojanin 1 and N-WASP, and functions in vesicle formation and transport. However, the mechanisms of action of PACSIN 1 in these processes are largely unknown. Here, full-length and five C-terminal truncation constructs of human PACSIN 1 have been successfully expressed and purified in Escherichia coli. PACSIN 1 (1–344) was crystallized and diffracted to a resolution of 3.0 Å. The crystal belonged to space group C2, with unit-cell parameters a = 158.65, b = 87.38, c = 91.76 Å, α = 90.00, β = 113.61, γ = 90.00°. There were two molecules in the asymmetric unit and the solvent content was estimated to be about 70.47%

Crystal growth, characterization and theoretical studies of alkaline earth metal-doped tetrakis(thiourea)nickel(II) chloride.

Science.gov (United States)

Agilandeshwari, R; Muthu, K; Meenatchi, V; Meena, K; Rajasekar, M; Aditya Prasad, A; Meenakshisundaram, S P

2015-02-25

The influence of Sr(II)-doping on the properties of tetrakis(thiourea)nickel(II) chloride (TTNC) has been described. The reduction in the intensity observed in powder X-ray diffraction of doped specimen and slight shifts in vibrational frequencies of doped specimens confirm the lattice stress as a result of doping. Surface morphological changes due to doping of the Sr(II) are observed by scanning electron microscopy. The incorporation of metal into the host crystal lattice was confirmed by energy dispersive X-ray spectroscopy. Lattice parameters are determined by single crystal XRD analysis. The thermogravimetric and differential thermal analysis studies reveal the purity of the materials and no decomposition is observed up to the melting point. The nonlinear optical properties of the doped and undoped specimens were studied. Theoretical calculations were performed using the Density functional theory (DFT) method with B3LYP/LANL2DZ as the basis set. The molecular geometry and vibrational frequencies of TTNC in the ground state were calculated and the observed structural parameters of TTNC are compared with parameters obtained from single crystal X-ray studies. The atomic charge distributions are obtained by Mulliken charge population analysis. The first-order molecular hyperpolarizability, polarizability and dipole moment were derived. Copyright © 2014 Elsevier B.V. All rights reserved.

Crystal growth, spectroscopic and laser properties of Tm:LuAG crystal

Science.gov (United States)

Xu, X. D.; Wang, X. D.; Lin, Z. F.; Cheng, Y.; Li, D. Z.; Cheng, S. S.; Wu, F.; Zhao, Z. W.; Gao, C. Q.; Gao, M. W.; Xu, J.

2009-11-01

Tm:Lu3Al5O12 (Tm:LuAG) crystal was grown by the Czochralski method. The segregation coefficient was measured by Inductively Coupled Plasma Atomic Emission Spectrometer. The cell parameters were analyzed with X-ray powder diffraction experiments. The absorption and fluorescence spectra of Tm:LuAG crystal at room temperature were investigated. With a 20 W fiber-coupled diode laser as pump source, the continuous-wave (CW) laser action of Tm:LuAG crystal was demonstrated. The maximum output power at 2020 nm was obtained to be 3.04 W, and the slope efficiency was 25.3%.

Expression, purification, crystallization and preliminary X-ray diffraction analysis of nurse shark β2-microglobulin

International Nuclear Information System (INIS)

Lu, Shuangshuang; Yao, Shugang; Chen, Rong; Zhang, Nianzhi; Chen, Jianmin; Gao, Feng; Xia, Chun

2012-01-01

A crystal of nurse shark β 2 -microglobulin diffracted to 2.3 Å resolution and belonged to space group P3 2 21, with unit-cell parameters a = b = 88.230, c = 67.146 Å and two molecules per asymmetric unit. The Matthews coefficient V M was calculated to be about 3.28 Å 3 Da −1 , corresponding to 62.5% solvent content. β 2 -Microglobulin (β 2 m) is an essential subunit of the major histocompatibility complex (MHC) class I molecule that helps to stabilize the structure of peptide–MHC I (pMHC I). It is also one of the typical immunoglobulin superfamily (IgSF) molecules in the adaptive immune system (AIS). Sharks belong to the cartilaginous fish, which are the oldest jawed vertebrate ancestors with an AIS to exist in the world. Thus, the study of cartilaginous fish β 2 m would help in understanding the evolution of IgSF molecules. In order to demonstrate this, β 2 m from a cartilaginous fish, nurse shark (Ginglymostoma cirratum), was expressed, refolded, purified and crystallized. Diffraction data were collected to a resolution of 2.3 Å. The crystal belonged to space group P3 2 21, with unit-cell parameters a = b = 88.230, c = 67.146 Å. The crystal structure contained two molecules in the asymmetric unit. The results will provide structural information for study of the evolution of β 2 m and IgSF in the AIS

Sensitivity analysis in multi-parameter probabilistic systems

International Nuclear Information System (INIS)

Walker, J.R.

1987-01-01

Probabilistic methods involving the use of multi-parameter Monte Carlo analysis can be applied to a wide range of engineering systems. The output from the Monte Carlo analysis is a probabilistic estimate of the system consequence, which can vary spatially and temporally. Sensitivity analysis aims to examine how the output consequence is influenced by the input parameter values. Sensitivity analysis provides the necessary information so that the engineering properties of the system can be optimized. This report details a package of sensitivity analysis techniques that together form an integrated methodology for the sensitivity analysis of probabilistic systems. The techniques have known confidence limits and can be applied to a wide range of engineering problems. The sensitivity analysis methodology is illustrated by performing the sensitivity analysis of the MCROC rock microcracking model

Purification, crystallization and preliminary crystallographic analysis of SMU.1108c protein from Streptococcus mutans

International Nuclear Information System (INIS)

Feng, Ming-Jing; Fu, Tian-Min; Liu, Xiang; Li, Lan-Fen

2010-01-01

SMU.1108c, a putative uncharacterized protein from S. mutans, was crystallized and X-ray diffraction data were collected to a resolution of 2.2 Å. Streptococcus mutans SMU.1108c (KEGG database) encodes a functionally uncharacterized protein consisting of 270 amino-acid residues. This protein is predicted to have a haloacid dehalogenase hydrolase-like domain and is a homologue of haloacid dehalogenase phosphatases that catalyze phosphoryl-transfer reactions. In this work, SMU.1108c was cloned into the pET28a vector and overexpressed in Escherichia coli strain BL21 (DE3). The protein was purified to homogeneity and crystallized using the sitting-drop vapour-diffusion method. The best crystal diffracted to 2.0 Å resolution and belonged to space group C2, with unit-cell parameters a = 77.1, b = 80.2, c = 47.9 Å, β = 99.5°

Expression, Purification, Crystallization and Preliminary X-ray Analysis of Pseudomonas fluorescens AlgK

Energy Technology Data Exchange (ETDEWEB)

Keiski,C.; Yip, P.; Robinson, H.; Burrows, L.; Howell, P.

2007-01-01

AlgK is an outer-membrane lipoprotein involved in the biosynthesis of alginate in Pseudomonads and Azotobacter vinelandii. A recombinant form of Pseudomonas fluorescens AlgK with a C-terminal polyhistidine affinity tag has been expressed and purified from the periplasm of Escherichia coli cells and diffraction-quality crystals of AlgK have been grown using the hanging-drop vapour-diffusion method. The crystals grow as flat plates with unit-cell parameters a = 79.09, b = 107.85, c = 119.15 {angstrom}, = 96.97{sup o}. The crystals exhibit the symmetry of space group P2{sub 1} and diffract to a minimum d-spacing of 2.5 {angstrom} at Station X29 of the National Synchrotron Light Source, Brookhaven National Laboratory. On the basis of the Matthews coefficient (V{sub M} = 2.53 {angstrom}{sup 3} Da{sup -1}), four protein molecules are estimated to be present in the asymmetric unit.

Phononic crystals fundamentals and applications

CERN Document Server

Adibi, Ali

2016-01-01

This book provides an in-depth analysis as well as an overview of phononic crystals. This book discusses numerous techniques for the analysis of phononic crystals and covers, among other material, sonic and ultrasonic structures, hypersonic planar structures and their characterization, and novel applications of phononic crystals. This is an ideal book for those working with micro and nanotechnology, MEMS (microelectromechanical systems), and acoustic devices. This book also: Presents an introduction to the fundamentals and properties of phononic crystals Covers simulation techniques for the analysis of phononic crystals Discusses sonic and ultrasonic, hypersonic and planar, and three-dimensional phononic crystal structures Illustrates how phononic crystal structures are being deployed in communication systems and sensing systems.

Crystallization and preliminary crystallographic analysis of d-alanine-d-alanine ligase from Streptococcus mutans

Energy Technology Data Exchange (ETDEWEB)

Lu, Yong-Zhi; Sheng, Yu [Institute for Nanobiomedical Technology and Membrane Biology, West China Hospital, Sichuan University, Chengdu 610065, Sichuan (China); Li, Lan-Fen [National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871 (China); Tang, De-Wei [Institute for Nanobiomedical Technology and Membrane Biology, West China Hospital, Sichuan University, Chengdu 610065, Sichuan (China); Liu, Xiang-Yu [National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871 (China); Zhao, Xiaojun, E-mail: zhaoxj@scu.edu.cn [Institute for Nanobiomedical Technology and Membrane Biology, West China Hospital, Sichuan University, Chengdu 610065, Sichuan (China); Liang, Yu-He, E-mail: zhaoxj@scu.edu.cn; Su, Xiao-Dong [National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871 (China); Institute for Nanobiomedical Technology and Membrane Biology, West China Hospital, Sichuan University, Chengdu 610065, Sichuan (China)

2007-09-01

A potential target for antibiotic drug design, d-alanine-d-alanine ligase from S. mutans, was expressed in E. coli, purified and crystallized. Diffraction data were collected to 2.4 Å resolution. d-Alanine-d-alanine ligase is encoded by the gene ddl (SMU-599) in Streptococcus mutans. This ligase plays a very important role in cell-wall biosynthesis and may be a potential target for drug design. To study the structure and function of this ligase, the gene ddl was amplified from S. mutans genomic DNA and cloned into the expression vector pET28a. The protein was expressed in soluble form in Escherichia coli strain BL21 (DE3). Homogeneous protein was obtained using a two-step procedure consisting of Ni{sup 2+}-chelating and size-exclusion chromatography. Purified protein was crystallized and the cube-shaped crystal diffracted to 2.4 Å. The crystal belongs to space group P3{sub 1}21 or P3{sub 2}21, with unit-cell parameters a = b = 79.50, c = 108.97 Å. There is one molecule per asymmetric unit.

Crystallization and preliminary crystallographic analysis of d-alanine-d-alanine ligase from Streptococcus mutans

International Nuclear Information System (INIS)

Lu, Yong-Zhi; Sheng, Yu; Li, Lan-Fen; Tang, De-Wei; Liu, Xiang-Yu; Zhao, Xiaojun; Liang, Yu-He; Su, Xiao-Dong

2007-01-01

A potential target for antibiotic drug design, d-alanine-d-alanine ligase from S. mutans, was expressed in E. coli, purified and crystallized. Diffraction data were collected to 2.4 Å resolution. d-Alanine-d-alanine ligase is encoded by the gene ddl (SMU-599) in Streptococcus mutans. This ligase plays a very important role in cell-wall biosynthesis and may be a potential target for drug design. To study the structure and function of this ligase, the gene ddl was amplified from S. mutans genomic DNA and cloned into the expression vector pET28a. The protein was expressed in soluble form in Escherichia coli strain BL21 (DE3). Homogeneous protein was obtained using a two-step procedure consisting of Ni 2+ -chelating and size-exclusion chromatography. Purified protein was crystallized and the cube-shaped crystal diffracted to 2.4 Å. The crystal belongs to space group P3 1 21 or P3 2 21, with unit-cell parameters a = b = 79.50, c = 108.97 Å. There is one molecule per asymmetric unit

Expression, purification, crystallization and X-ray analysis of 3-quinuclidinone reductase from Agrobacterium tumefaciens

International Nuclear Information System (INIS)

Hou, Feng; Miyakawa, Takuya; Takeshita, Daijiro; Kataoka, Michihiko; Uzura, Atsuko; Nagata, Koji; Shimizu, Sakayu; Tanokura, Masaru

2012-01-01

The purification and crystallization of 3-quinuclidinone reductase from A. tumefaciens allowed the collection of a diffraction data set to 1.72 Å resolution. (R)-3-Quinuclidinol is a useful chiral building block for the synthesis of various pharmaceuticals and can be produced from 3-quinuclidinone by asymmetric reduction. A novel 3-quinuclidinone reductase from Agrobacterium tumefaciens (AtQR) catalyzes the stereospecific reduction of 3-quinuclidinone to (R)-3-quinuclidinol with NADH as a cofactor. Recombinant AtQR was overexpressed in Escherichia coli, purified and crystallized with NADH using the sitting-drop vapour-diffusion method at 293 K. Crystals were obtained using a reservoir solution containing PEG 3350 as a precipitant. X-ray diffraction data were collected to 1.72 Å resolution on beamline BL-5A at the Photon Factory. The crystal belonged to space group P2 1 , with unit-cell parameters a = 62.0, b = 126.4, c = 62.0 Å, β = 110.5°, and was suggested to contain four molecules in the asymmetric unit (V M = 2.08 Å 3 Da −1 )

Zr 2Ir 6B with an eightfold superstructure of the cubic perovskite-like boride ZrIr 3B 0.5: Synthesis, crystal structure and bonding analysis

Science.gov (United States)

Hermus, Martin; Fokwa, Boniface P. T.

2010-04-01

Single phase powder samples and single crystals of Zr 2Ir 6B were successfully synthesized by arc-melting the elements in a water-cooled copper crucible under an argon atmosphere. Superstructure reflections were observed both on powder and on single crystal diffraction data, leading to an eightfold superstructure of ZrIr 3B x phase. The new phase, which has a metallic luster, crystallizes in space group Fm3¯m (no. 225) with the lattice parameters a=7.9903(4) Å, V=510.14(4) Å 3. Its crystal structure was refined on the basis of powder as well as single crystal data. The single crystal refinement converged to R1=0.0239 and w R2=0.0624 for all 88 unique reflections and 6 parameters. Zr 2Ir 6B is isotypic to Ti 2Rh 6B and its structure can be described as a defect double perovskite, A2BB' O6, where the A site is occupied by zirconium, the B site by boron, the O site by iridium but the B' site is vacant, leading to the formation of empty and boron-filled octahedral Ir 6 clusters. According to the result of tight-binding electronic structure calculations, Ir-B and Ir-Zr interactions are mainly responsible for the structural stability of the phase. According to COHP bonding analysis, the strongest bonding occurs for the Ir-B contacts, and the Ir-Ir bonding within the empty clusters is two times stronger than that in the BIr 6 octahedra.

Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of chlorite dismutase: a detoxifying enzyme producing molecular oxygen

Energy Technology Data Exchange (ETDEWEB)

Geus, Daniël C. de, E-mail: d.de.geus@chem.leidenuniv.nl; Thomassen, Ellen A. J.; Feltz, Clarisse L. van der; Abrahams, Jan Pieter [Biophysical Structural Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden (Netherlands)

2008-08-01

Preliminary X-ray data collection and analysis for crystals of chlorite dismutase, a haem-based enzyme that very effectively reduces chlorite to chloride while producing molecular oxygen, is reported to 2.1 Å resolution. Chlorite dismutase, a homotetrameric haem-based protein, is one of the key enzymes of (per)chlorate-reducing bacteria. It is highly active (< 2 kU mg{sup −1}) in reducing the toxic compound chlorite to the innocuous chloride anion and molecular oxygen. Chlorite itself is produced as the intermediate product of (per)chlorate reduction. The chlorite dismutase gene in Azospira oryzae strain GR-1 employing degenerate primers has been identified and the active enzyme was subsequently overexpressed in Escherichia coli. Chlorite dismutase was purified, proven to be active and crystallized using sitting drops with PEG 2000 MME, KSCN and ammonium sulfate as precipitants. The crystals belonged to space group P2{sub 1}2{sub 1}2 and were most likely to contain six subunits in the asymmetric unit. The refined unit-cell parameters were a = 164.46, b = 169.34, c = 60.79 Å. The crystals diffracted X-rays to 2.1 Å resolution on a synchrotron-radiation source and a three-wavelength MAD data set has been collected. Determination of the chlorite dismutase structure will provide insights into the active site of the enzyme, for which no structures are currently available.

Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of glyoxalase I from Leishmania infantum

International Nuclear Information System (INIS)

Barata, Lídia; Sousa Silva, Marta; Schuldt, Linda; Costa, Gonçalo da; Tomás, Ana M.; Ferreira, António E. N.; Weiss, Manfred S.; Ponces Freire, Ana; Cordeiro, Carlos

2010-01-01

Glyoxalase I from L. infantum was cloned, overexpressed in E. coli, purified and crystallized. Glyoxalase I (GLO1) is the first of the two glyoxalase-pathway enzymes. It catalyzes the formation of S-d-lactoyltrypanothione from the non-enzymatically formed hemithioacetal of methylglyoxal and reduced trypanothione. In order to understand its substrate binding and catalytic mechanism, GLO1 from Leishmania infantum was cloned, overexpressed in Escherichia coli, purified and crystallized. Two crystal forms were obtained: a cube-shaped form and a rod-shaped form. While the cube-shaped form did not diffract X-rays at all, the rod-shaped form exhibited diffraction to about 2.0 Å resolution. The crystals belonged to space group P2 1 2 1 2, with unit-cell parameters a = 130.03, b = 148.51, c = 50.63 Å and three dimers of the enzyme per asymmetric unit

Design of Double PG Crystal Neutron Diffractometer

International Nuclear Information System (INIS)

Adib, M.; Habib, N.; El-Mesiry, M.S.; Fathallah, M.

2011-01-01

The design of a diffractometer containing two pyrolytic graphite (PG) crystals to select monochromatic neutrons in the range of wavelengths longer than 0.26 nm is given. The first crystal is high oriented pyrolytic graphite (HOPG) set at glancing angle to reflect monochromatic neutrons with a selected wavelength. The second is a low quality PG crystal filter, set at take-off-angle such that, it transmits the selected monochromatic neutrons and rejects the higher order contaminations accompanying the first order reflection. It was shown that, 2 mm thick of PG crystal having 0.30 FWHM on mosaic spread are the optimum parameters of monochromator PG crystal. While the optimum thickness and mosaic spread of the PG crystal filter were selected to have low contamination factor of higher order reflections. The optimum parameters of the PG filter crystal were calculated using the computer package Graphite recently developed in our laboratory. Calculation shows that, 3 cm thick PG filter (20 on mosaic spread) is sufficient to almost eliminate the higher order contaminations accompanying the main monochromatic neutrons with

Crystallization and preliminary X-ray characterization of a ferritin from the hyperthermophilic archaeon and anaerobe Pyrococcus furiosus

International Nuclear Information System (INIS)

Matias, Pedro M.; Tatur, Jana; Carrondo, Maria Arménia; Hagen, Wilfred R.

2005-01-01

Ferritin from P. furiosus crystallizes in space group C222 1 , with unit-cell parameters a = 258.1, b = 340.1, c = 266.5 Å and 36 monomers in the asymmetric unit, corresponding to one and a half 24-mers. Crystals of the title protein have been produced and preliminary structural analysis has been carried out. The crystals belong to the orthorhombic space group C222 1 , with unit-cell parameters a = 258.1, b = 340.1, c = 266.5 Å. The protein forms a 24-mer of 20 kDa subunits, which assemble with 432 non-crystallographic symmetry. A total of 36 monomers are found in the asymmetric unit, corresponding to one and a half 24-mers

Overexpression, crystallization and preliminary X-ray analysis of xylulose-5-phosphate/fructose-6-phosphate phosphoketolase from Bifidobacterium breve

International Nuclear Information System (INIS)

Suzuki, Ryuichiro; Kim, Byung-Jun; Shibata, Tsuyoshi; Iwamoto, Yuki; Katayama, Takane; Ashida, Hisashi; Wakagi, Takayoshi; Shoun, Hirofumi; Fushinobu, Shinya; Yamamoto, Kenji

2010-01-01

Xylulose-5-phosphate/fructose-6-phosphate phosphoketolase from B. breve was overexpressed and crystallized. The crystals belonged to the tetragonal space group I422 and diffracted to beyond 1.7 Å resolution. The xylulose-5-phosphate/fructose-6-phosphate phosphoketolase gene from Bifidobacterium breve was cloned and overexpressed in Escherichia coli. The enzyme was purified to homogeneity and crystallized by the sitting-drop vapour-diffusion method. Crystals were obtained at 293 K using 0.05 mM thiamine diphosphate, 0.25 mM MgCl 2 , 24%(w/v) PEG 6000 and 0.1 M Bicine pH 9.0. The crystals belonged to the tetragonal space group I422, with unit-cell parameters a = b = 174.8, c = 163.8 Å, and diffracted to beyond 1.7 Å resolution

Protein preparation, crystallization and preliminary X-ray analysis of Trypanosoma cruzi nucleoside diphosphate kinase 1

International Nuclear Information System (INIS)

Gómez Barroso, J. A.; Pereira, H.; Miranda, M.; Pereira, C.; Garratt, R. C.; Aguilar, C. F.

2010-01-01

T. cruzi TcNDPK1 was overexpressed in Escherichia coli as an N-terminally poly-His-tagged fusion protein and crystallized. The flagellated protozoan parasite Trypanosoma cruzi is the aetiological agent of Chagas disease. Nucleoside diphosphate kinases (NDPKs) are enzymes that are involved in energy management and nucleoside balance in the cell. T. cruzi TcNDPK1, a canonical isoform, was overexpressed in Escherichia coli as an N-terminally poly-His-tagged fusion protein and crystallized. Crystals grew after 72 h in 0.2 M MgCl 2 , 20% PEG 3350. Data were collected to 3.5 Å resolution using synchrotron X-ray radiation at the National Synchrotron Light Laboratory (Campinas, Brazil). The crystals belonged to the trigonal space group P3, with unit-cell parameters a = b = 127.84, c = 275.49 Å. Structure determination is under way and will provide relevant information that may lead to the first step in rational drug design for the treatment of Chagas disease

Crystallization and Preliminary X-ray Analysis of Bacteriophasge T4 UvsY Recombination Mediator Protein

International Nuclear Information System (INIS)

Xu, H.; Beernink, H.; Rould, M.; Morrical, S.

2006-01-01

Bacteriophage T4 UvsY protein is considered to be the prototype of recombination mediator proteins, a class of proteins which assist in the loading of recombinases onto DNA. Wild-type and Se-substituted UvsY protein have been expressed and purified and crystallized by hanging-drop vapor diffusion. The crystals diffract to 2.4 (angstrom) using in-house facilities and to 2.2 (angstrom) at NSLS, Brookhaven National Laboratory. The crystals belong to space group P422, P4 2 22, P42 1 2 or P4 2 2 1 2, the ambiguity arising from pseudo-centering, with unit-cell parameters a = b = 76.93, c = 269.8 (angstrom). Previous biophysical characterization of UvsY indicates that it exists primarily as a hexamer in solution. Along with the absence of a crystallographic threefold, this suggests that the asymmetric unit of these crystals is likely to contain either three monomers, giving a solvent content of 71%, or six monomers, giving a solvent content of 41%

Purification, crystallization and preliminary crystallographic analysis of the minor pilin FctB from Streptococcus pyogenes

International Nuclear Information System (INIS)

Linke, Christian; Young, Paul G.; Kang, Hae Joo; Proft, Thomas; Baker, Edward N.

2010-01-01

The minor pilin FctB from S. pyogenes strain 90/306S was expressed in E. coli, purified and crystallized. The hexagonal FctB crystals diffracted to 2.9 Å resolution. The minor pilin FctB is an integral part of the pilus assembly expressed by Streptococcus pyogenes. Since it is located at the cell wall, it can be hypothesized that it functions as a cell-wall anchor for the streptococcal pilus. In order to elucidate its structure, the genes for FctB from the S. pyogenes strains 90/306S and SF370 were cloned for overexpression in Escherichia coli. FctB from strain 90/306S was crystallized by the sitting-drop vapour-diffusion method using sodium citrate as a precipitant. The hexagonal FctB crystals belonged to space group P6 1 or P6 5 , with unit-cell parameters a = b = 95.15, c = 100.25 Å, and diffracted to 2.9 Å resolution

Growth and characterization of hexaaquacobalt(II) dipotassium tetrahydrogen tetra-o-phthalate tetrahydrate crystals

Energy Technology Data Exchange (ETDEWEB)

Muthu, K. [Department of Chemistry, Annamalai University, Annamalainagar 608 002 (India); Bhagavannarayana, G. [National Physical Laboratory (CSIR), New Delhi 110 012 (India); Mahadevan, C.K. [Physics Research Centre, S.T. Hindu College, Nagercoil 629002 (India); Meenakshisundaram, S.P., E-mail: aumats2009@gmail.com [Department of Chemistry, Annamalai University, Annamalainagar 608 002 (India)

2013-05-15

Single crystals of hexaaquacobalt(II) dipotassium tetrahydrogen tetra-o-phthalate tetrahydrate K{sub 2}[Co(H{sub 2}O){sub 6}](C{sub 8}H{sub 5}O{sub 4}){sub 4}·4H{sub 2}O (PCHP), a semiorganic light-rose colored crystal of size ∼38 × 16 × 4 mm{sup 3} have been grown by slow evaporation solution growth technique. The lattice parameters of the as-grown crystals were obtained by single crystal X-ray diffraction analysis. The functional groups of the phthalate complex were confirmed by Fourier transform infrared spectroscopy analysis. The UV–Vis optical absorption spectrum of PCHP shows the lower optical cut-off at ∼300 nm and the crystal was transparent in the visible region. The structural perfection of the grown crystal has been analyzed by high-resolution X-ray diffraction (HRXRD) rocking curves (DC). The DC contains multi-peaks showing the structural grain boundaries. The dielectric, thermal and mechanical behaviors of the specimen were also studied. - Highlights: ► Bulk growth of large size phthalate complex crystals. ► Crystalline perfection of the grown crystal has been determined. ► HRXRD curves compared with pure material and the reasons are analyzed.

Crystallization and preliminary X-ray analysis of the complexes between a Fab and two forms of human insulin-like growth factor II

International Nuclear Information System (INIS)

Newman, Janet; Cohen, Edward H.; Cosgrove, Leah; Kopacz, Kris; Dransfield, Daniel T.; Adams, Timothy E.; Peat, Thomas S.

2009-01-01

Complexes of both hIGF-II and hIGF-IIE with a Fab have been crystallized and investigated by X-ray analysis. Elevated expression of insulin-like growth factor II (IGF-II) is frequently observed in a variety of human malignancies, including breast, colon and liver cancer. As IGF-II can deliver a mitogenic signal through both the type 1 insulin-like growth factor receptor (IGF-IR) and an alternately spliced form of the insulin receptor (IR-A), neutralizing the biological activity of this growth factor directly is an attractive therapeutic option. One method of doing this would be to find antibodies that bind tightly and specifically to the peptide, which could be used as protein therapeutics to lower the peptide levels in vivo and/or to block the peptide from binding to the IGF-IR or IR-A. To address this, Fabs were selected from a phage-display library using a biotinylated precursor form of the growth factor known as IGF-IIE as a target. Fabs were isolated that were specific for the E-domain C-terminal extension and for mature IGF-II. Four Fabs selected from the library were produced, complexed with IGF-II and set up in crystallization trials. One of the Fab–IGF-II complexes (M64-F02–IGF-II) crystallized readily, yielding crystals that diffracted to 2.2 Å resolution and belonged to space group P2 1 2 1 2 1 , with unit-cell parameters a = 50.7, b = 106.9, c = 110.7 Å. There was one molecule of the complete complex in the asymmetric unit. The same Fab was also crystallized with a longer form of the growth factor, IGF-IIE. This complex crystallized in space group P2 1 2 1 2 1 , with unit-cell parameters a = 50.7, b = 107, c = 111.5 Å, and also diffracted X-rays to 2.2 Å resolution

Crystal growth and properties of novel organic nonlinear optical crystals of 4-Nitrophenol urea

Energy Technology Data Exchange (ETDEWEB)

Mohan, M. Krishna, E-mail: krishnamohan.m@ktr.srmuniv.ac.in; Ponnusamy, S.; Muthamizhchelvan, C.

2017-07-01

Single crystals of 4-Nitrophenol urea have been grown from water using slow evaporation technique at constant temperature, with the vision to improve the properties of the crystals. The unit cell parameters of the grown crystals were determined by single crystal and powder X-Ray diffraction. FTIR studies reveals the presence of different vibrational bands. The Optical studies confirmed that the crystal is transparent up to 360 nm .TGA and DSC studies were carried out to understand the thermal behavior of crystals. The SHG studies show the suitability of the crystals for NLO applications. The etching studies were carried out to study the behavior of the crystals under different conditions.These studies reveal that the crystals of 4-Nitrophenol urea are suitable for device applications. - Highlights: • 4-Nitrophenol urea crystals of dimensions 14 mm × 1 mm were grown. • UV–Visible studies indicate the crystal is transparent in the region of 370–800 nm. • Thermal studies show the crystal starts decomposing at 170 °C. • SHG studies indicate that the crystals have NLO efficiency 3.5 times that of KDP.

Crystallization and preliminary X-ray crystallographic analysis of enoyl-ACP reductase III (FabL) from Bacillus subtilis

International Nuclear Information System (INIS)

Kim, Kook-Han; Park, Joon Kyu; Ha, Byung Hak; Moon, Jin Ho; Kim, Eunice EunKyeong

2007-01-01

Enoyl-ACP reductase III (FabL) from B. subtilis has been overexpressed, purified and crystallized. The crystal belongs to space group P622, with unit-cell parameters a = b = 139.56, c = 62.75 Å, α = β = 90, γ = 120°, and data were collected to 2.5 Å resolution using synchrotron radiation. Enoyl-[acyl-carrier protein] reductase (enoyl-ACP reductase; ENR) is a key enzyme in type II fatty-acid synthase that catalyzes the last step in each elongation cycle. It has been considered as an antibiotic target since it is an essential enzyme in bacteria. However, recent studies indicate that some pathogens have more than one ENR. Bacillus subtilis is reported to have two ENRs, namely BsFabI and BsFabL. While BsFabI is similar to other FabIs, BsFabL shows very little sequence similarity and is NADPH-dependent instead of NADH-dependent as in the case of FabI. In order to understand these differences on a structural basis, BsFabL has been cloned, expressed and and crystallized. The crystal belongs to space group P622, with unit-cell parameters a = b = 139.56, c = 62.75 Å, α = β = 90, γ = 120° and one molecule of FabL in the asymmetric unit. Data were collected using synchrotron radiation (beamline 4A at the Pohang Light Source, Korea). The crystal diffracted to 2.5 Å resolution

Expression, purification, crystallization and preliminary X-ray analysis of the human RuvB-like protein RuvBL1

International Nuclear Information System (INIS)

Gorynia, Sabine; Matias, Pedro M.; Gonçalves, Susana; Coelho, Ricardo; Lopes, Gonçalo; Thomaz, Mónica; Huber, Martina; Haendler, Bernard; Donner, Peter; Carrondo, Maria Arménia

2005-01-01

Human RuvB-like protein RuvBL1 plays important roles in essential signaling pathways like c-Myc and Wnt, in transcription, and in DNA repair and apoptosis. Crystals of both native and a Se-Met derivative were obtained and characterized. SAD data leading to the structure solution at 2.2 Å were measured from the Se-Met crystals. RuvBL1, an evolutionary highly conserved protein related to the AAA + family of ATPases, has been crystallized using the hanging-drop vapour-diffusion method at 293 K. The crystals are hexagonal and belong to space group P6, with unit-cell parameters a = b = 207.1, c = 60.7 Å and three molecules in the asymmetric unit

Preliminary X-ray analysis of twinned crystals of the Q88Y25-Lacpl esterase from Lactobacillus plantarum WCFS1

International Nuclear Information System (INIS)

Álvarez, Yanaisis; Esteban-Torres, María; Acebrón, Iván; Rivas, Blanca de las; Muñoz, Rosario; Martínez-Ripoll, Martín; Mancheño, José M.

2011-01-01

The Q88Y25-Lacpl esterase from L. plantarum WCFS1 has been recombinantly expressed, purified and crystallized. A native diffraction data set has been collected to 2.24 Å resolution. Q88Y25-Lacpl is an esterase produced by the lactic acid bacterium Lactobacillus plantarum WCFS1 that shows amino-acid sequence similarity to carboxylesterases from the hormone-sensitive lipase family, in particular the AFEST esterase from the archaeon Archaeoglobus fulgidus and the hyperthermophilic esterase EstEI isolated from a metagenomic library. N-terminally His 6 -tagged Q88Y25-Lacpl has been overexpressed in Escherichia coli BL21 (DE3) cells, purified and crystallized at 291 K using the hanging-drop vapour-diffusion method. Mass spectrometry was used to determine the purity and homogeneity of the enzyme. Crystals of His 6 -tagged Q88Y25-Lacpl were prepared in a solution containing 2.8 M sodium acetate trihydrate pH 7.0. X-ray diffraction data were collected to 2.24 Å resolution on beamline ID29 at the ESRF. The apparent crystal point group was 422; however, initial global analysis of the intensity statistics (data processed with high symmetry in space group I422) and subsequent tests on data processed with low symmetry (space group I4) showed that the crystals were almost perfectly merohedrally twinned. Most probably, the true space group is I4, with unit-cell parameters a = 169.05, b = 169.05, c = 183.62 Å

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

International Nuclear Information System (INIS)

Krejčiříková, Veronika; Fábry, Milan; Marková, Vladimíra; Malý, Petr; Řezáčová, Pavlína; Brynda, Jiří

2008-01-01

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 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 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

Crystallization and preliminary X-ray crystallographic analysis of highly thermostable L2 lipase from the newly isolated Bacillus sp. L2

International Nuclear Information System (INIS)

Shariff, Fairolniza Mohd; Rahman, Raja Noor Zaliha Raja Abd.; Ali, Mohd Shukuri Mohamad; Chor, Adam Leow Thean; Basri, Mahiran; Salleh, Abu Bakar

2010-01-01

Thermostable recombinant L2 lipase from thermophilic Bacillus sp. L2 has been crystallized by using counter-diffusion method and diffracted to 2.7 Å resolution. The crystal belongs to the primitive orthorhombic space group P2 1 2 1 2 1 with unit-cell parameters a = 87.44, b = 94.90, c = 126.46 Å. Purified thermostable recombinant L2 lipase from Bacillus sp. L2 was crystallized by the counter-diffusion method using 20% PEG 6000, 50 mM MES pH 6.5 and 50 mM NaCl as precipitant. X-ray diffraction data were collected to 2.7 Å resolution using an in-house Bruker X8 PROTEUM single-crystal diffractometer system. The crystal belonged to the primitive orthorhombic space group P2 1 2 1 2 1 , with unit-cell parameters a = 87.44, b = 94.90, c = 126.46 Å. The asymmetric unit contained one single molecule of protein, with a Matthews coefficient (V M ) of 2.85 Å 3 Da −1 and a solvent content of 57%

Structure analysis on synthetic emerald crystals

Science.gov (United States)

Lee, Pei-Lun; Lee, Jiann-Shing; Huang, Eugene; Liao, Ju-Hsiou

2013-05-01

Single crystals of emerald synthesized by means of the flux method were adopted for crystallographic analyses. Emerald crystals with a wide range of Cr3+-doping content up to 3.16 wt% Cr2O3 were examined by X-ray single crystal diffraction refinement method. The crystal structures of the emerald crystals were refined to R 1 (all data) of 0.019-0.024 and w R 2 (all data) of 0.061-0.073. When Cr3+ substitutes for Al3+, the main adjustment takes place in the Al-octahedron and Be-tetrahedron. The effect of substitution of Cr3+ for Al3+ in the beryl structure results in progressively lengthening of the Al-O distance, while the length of the other bonds remains nearly unchanged. The substitution of Cr3+ for Al3+ may have caused the expansion of a axis, while keeping the c axis unchanged in the emerald lattice. As a consequence, the Al-O-Si and Al-O-Be bonding angles are found to decrease, while the angle of Si-O-Be increases as the Al-O distance increases during the Cr replacement.

Design of glass-ceramic complex microstructure with using onset point of crystallization in differential thermal analysis

International Nuclear Information System (INIS)

Hwang, Seongjin; Kim, Jinho; Shin, Hyo-Soon; Kim, Jong-Hee; Kim, Hyungsun

2008-01-01

Two types of frits with different compositions were used to develop a high strength substrate in electronic packaging using a low temperature co-fired ceramic process. In order to reveal the crystallization stage during heating to approximately 900 deg. C, a glass-ceramic consisting of the two types of frits, which had been crystallized to diopside and anorthite after firing, was tested at different mixing ratios of the frits. The exothermal peaks deconvoluted by a Gauss function in the differential thermal analysis curves were used to determine the onset point of crystallization of diopside or anorthite. The onset points of crystallization were affected by the mixing ratio of the frits, and the microstructure of the glass-ceramic depended on the onset point of crystallization. It was found that when multicrystalline phases appear in the microstructure, the resulting complex microstructure could be predicted from the onset point of crystallization obtained by differential thermal analysis

Crystal growth, structural, optical, thermal, mechanical, laser damage threshold and electrical properties of triphenylphosphine oxide 4-nitrophenol (TP4N) single crystals for nonlinear optical applications

Science.gov (United States)

Karuppasamy, P.; Senthil Pandian, Muthu; Ramasamy, P.; Verma, Sunil

2018-05-01

, Lorentz-Lorentz equation, optical band gap and coupled dipole method (CDM). The Z-scan technique was carried out using solid state laser (640 nm) to analyze the nonlinear optical properties of the TP4N crystal. It exhibits the self-defocusing and saturable absorbance effect during analysis of closed and open aperture respectively. The nonlinear optical parameters such as refractive index (n2), absorption coefficient (β) and the third order nonlinear optical susceptibility (χ(3)) were analyzed.

Scale-free crystallization of two-dimensional complex plasmas: Domain analysis using Minkowski tensors

Science.gov (United States)