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Synchrotron X-ray Source (synchrotron + x-ray_source)
Selected AbstractsElucidation of zeolite microstructure by synchrotron X-ray diffuse scatteringJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2004B. J. Campbell Single-crystal diffuse scattering measurements can now rapidly probe the three-dimensional structure of subtle defects in microporous framework materials. Diffuse scattering data from natural mordenite crystals are shown to exhibit a complex distribution of weak features which have been mapped out using a synchrotron X-ray source and a CCD detector. Comparison with computer-simulated diffuse scattering patterns yields a detailed three-dimensional columnar defect structure and reveals that roughly one third of the mordenite's columnar defects cooperate to form a block-mosaic pattern of {110} stacking faults. [source] DIATOM SILICA BIOMINERALIZATION: AT NANOSCALE LEVEL A CHEMICALLY UNIFORM PROCESSJOURNAL OF PHYCOLOGY, Issue 2000E. G. Vrieling Using a high-brilliance synchrotron X-ray source, combined small- and wide-angle X-ray scattering (SAXS and WAXS) was applied to study nanoscale characteristics, in particular pore size in the range of 3 to 65 nm, of a variety of unialgal cultures of centric and pennate diatoms, and of mixed diatom populations sampled in the field. Results of scattering analysis were compared with details of pore size, structure and orientation visible at the electron microscopic level. WAXS patterns did not reveal any crystalline phase or features of microcrystallinity (resolution 0.07 to 0.51 nm), which implies a totally amorphous character of the SiO2 matrix of the frustule material. SAXS data (resolution 3 to 65 nm) provided information on geometry, size, and distribution of pores in the silica. Overall, two pore regions were recognized that were common to the silica of all samples: the smallest (d less than 10 nm) regularly spaced and shaped spherically, the larger (up to 65 nm) being cylinders or slits. Apparently, at a nanoscale level diatomaceous silica is quite homologous among species, in agreement with the chemical principles of silica polymerization under the conditions of pH and precursor concentrations inside the silicon deposition vesicle. The final frustule "macro"-morphology is of course species-specific, being determined genetically. Synthetically-derived MCM-type silicas have a similarly organized pore distribution in an amorphous silica matrix as we found in all diatom species studied. We therefore suggest that organic molecules of a kind used as structure-directing agents to produce these artificial silicas play a role in the nucleation of the silica polymerization reaction and the shaping of pore morphology inside the silicon deposition vesicle of diatoms. Structure-directing molecules now await isolation from the SDV, followed by identification and characterisation by molecular techniques. [source] Phase-contrast X-ray imaging with a large monolithic X-ray interferometerJOURNAL OF SYNCHROTRON RADIATION, Issue 4 2000Tohoru Takeda To increase the field of view for large objects in phase-contrast X-ray imaging, a large monolithic X-ray interferometer has been fabricated using an available silicon ingot of diameter 10,cm. A performance study of this interferometer has been carried out using a synchrotron X-ray source. The view size of the interference pattern obtained with this interferometer was 25,mm wide and 15,mm high and its visibility was 79%. Various structures of a sliced human hepatocellular carcinoma were identified as necrosis, hemorrhagic necrosis, normal liver tissue and blood vessel. The performance of this interferometer was sufficient for phase-contrast X-ray imaging. [source] (K4Li4)Al8Ge8O32·8H2O: an Li+ -exchanged potassium aluminogermanate with the zeolite gismondine (GIS) topologyACTA CRYSTALLOGRAPHICA SECTION C, Issue 8 2003Aaron J. Celestian The title compound, lithium potassium dialuminium digermanium octaoxide dihydrate, (K,Li)-(Al,Ge)-GIS (GIS is gismondine), is the result of a 50% Li+ exchange into the K-(Al,Ge)-GIS structure. The (K,Li)-(Al,Ge)-GIS structure was determined from a 4,×,4,×,2,µm octahedral single crystal at the ESRF synchrotron X-ray source. The ion exchange results in a symmetry transformation from I2/a for K-(Al,Ge)-GIS to C2/c for (K,Li)-(Al,Ge)-GIS. The structural change is due to disordering of K+ ions with Li+ ions along the [001] channel and ordering of water molecules in the [101] channels. The distance between sites partially occupied by K+ ions increases from 2.19,(3),Å in K-(Al,Ge)-GIS to 2.94,(3),Å in (K,Li)-(Al,Ge)-GIS. The Li+ ions occupy positions along the twofold axis at the intersection of the eight-membered-ring channels in a twofold coordination with water molecules. For the four closest framework O2, anions, the Li,O distances are 3.87,(4),Å. [source] Crystallization and preliminary crystallographic analysis of endonuclease VIII in its uncomplexed formACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2004Gali Golan The Escherichia coli DNA repair enzyme endonuclease VIII (EndoVIII or Nei) excises oxidized pyrimidines from damaged DNA substrates. It overlaps in substrate specificity with endonuclease III and may serve as a back-up for this enzyme in E. coli. The three-dimensional structure of Nei covalently complexed with DNA has been recently determined, revealing the critical amino-acid residues required for DNA binding and catalytic activity. Based on this information, several site-specific mutants of the enzyme have been tested for activity against various substrates. Although the crystal structure of the DNA-bound enzyme has been fully determined, the important structure of the free enzyme has not previously been analyzed. In this report, the crystallization and preliminary crystallographic characterization of DNA-free Nei are described. Four different crystal habits are reported for wild-type Nei and two of its catalytic mutants. Despite being crystallized under different conditions, all habits belong to the same crystal form, with the same space group (I222) and a similar crystallographic unit cell (average parameters a = 57.7, b = 80.2, c = 169.7,Å). Two of these crystal habits, I and IV, appear to be suitable for full crystallographic analysis. Crystal habit I was obtained by vapour diffusion using PEG 8000, glycerol and calcium acetate. Crystal habit IV was obtained by a similar method using PEG 400 and magnesium chloride. Both crystals are mechanically strong and stable in the X-ray beam once frozen under cold nitrogen gas. A full diffraction data set has recently been collected from a wild-type Nei crystal of habit I (2.6,Å resolution, 85.2% completeness, Rmerge = 9.8%). Additional diffraction data were collected from an Nei-R252A crystal of habit IV (2.05,Å resolution, 99.9% completeness, Rmerge = 6.0%) and an Nei-E2A crystal of habit IV (2.25,Å resolution, 91.7% completeness, Rmerge = 6.2%). These diffraction data were collected at 95,100 K using a synchrotron X-ray source and a CCD area detector. All three data sets are currently being used to obtain crystallographic phasing via molecular-replacement techniques. [source] Crystallization and initial crystallographic analysis of phosphomannomutase/phosphoglucomutase from Pseudomonas aeruginosaACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2000Catherine A. Regni The enzyme phosphomannomutase/phosphoglucomutase (PMM/PGM) catalyzes the conversion of mannose 6-phosphate to mannose 1-phosphate in the second step of the alginate biosynthetic pathway of Pseudomonas aeruginosa. PMM/PGM has been crystallized by hanging-drop vapor diffusion in space group P212121. Crystals diffract to 1.75,Å resolution on a synchrotron X-ray source under cryo-cooling conditions. PMM/PGM substituted with selenomethionine has been purified and crystallizes isomorphously with the native enzyme. Structure determination by MAD phasing is under way. Because of its role in alginate biosynthesis, PMM/PGM is a potential target for therapeutic inhibitors to combat P. aeruginosa infections. [source] Crystallization and preliminary crystallographic analysis of poly-,-glutamate hydrolase from bacteriophage ,NIT1ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 9 2009Zui Fujimoto Particular Bacillus subtilis strains produce a capsular polypeptide poly-,-glutamate (,-PGA) that functions as a physical barrier against bacteriophage infection. Bacteriophage ,NIT1 can infect B. subtilis and produces a novel ,-PGA hydrolase PghP. PghP was overexpressed, purified and crystallized by the sitting-drop vapour-diffusion method. The crystals diffracted to a resolution of 2.4,Å using a synchrotron X-ray source and were found to belong to space group P3121 or P3221. [source] Preliminary X-ray crystallographic studies of yeast Get3ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2009Junbin Hu Tail-anchored (TA) proteins contain a single transmembrane domain (TMD) at the C-terminus. The post-translational insertion of TA proteins into the ER membrane requires the cooperation of the Golgi ER-trafficking (GET) complex, which contains Get1, Get2 and Get3. Get3 is a cytosolic ATPase which can recognize and bind the TMD of the TA proteins. Get1 and Get2 are ER transmembrane proteins which can recruit and form a complex with TA-bound Get3. The GET complex carries out an energy-dependent process that facilitates the insertion of the TA-protein TMD into the ER membrane. In order to investigate the mechanism by which the GET complex functions to promote protein insertion into the ER membrane, yeast Get3 has been crystallized. The crystals diffracted to 2.7,Å resolution using a synchrotron X-ray source. The crystals belonged to space group P21212, with unit-cell parameters a = 220.26, b = 112.95, c = 48.27,Å. There is one Get3 dimer in the asymmetric unit, which corresponds to a solvent content of approximately 65%. [source] Preliminary X-ray crystallographic studies of mouse UPR responsive protein P58(IPK) TPR fragmentACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 2 2008Jiahui Tao Endoplasmic reticulum (ER) stress induces the unfolded protein response (UPR), which can promote protein folding and misfolded protein degradation and attenuate protein translation and protein translocation into the ER. P58(IPK) has been proposed to function as a molecular chaperone to maintain protein-folding homeostasis in the ER under normal and stressed conditions. P58(IPK) contains nine TPR motifs and a C-terminal J-domain within its primary sequence. To investigate the mechanism by which P58(IPK) functions to promote protein folding within the ER, a P58(IPK) TPR fragment without the C-terminal J-domain was crystallized. The crystals diffract to 2.5,Å resolution using a synchrotron X-ray source. The crystals belong to space group P21, with unit-cell parameters a = 83.53, b = 92.75, c = 84.32,Å, , = 90.00, , = 119.36, , = 90.00°. There are two P58(IPK) molecules in the asymmetric unit, which corresponds to a solvent content of approximately 60%. Structure determination by MAD methods is under way. [source] Hard X-ray micro(spectro)scopy: A powerful tool for the geomicrobiologistsGEOBIOLOGY, Issue 3 2008K. M. KEMNER ABSTRACT During the past few decades, the use of electron microscopy approaches , many developed by Terry Beveridge , to probe the physiology of microorganisms has become a mainstay in fields including microbiology, human health, and geomicrobiology. Recent developments of third-generation synchrotron X-ray sources and X-ray-based microscopy approaches for studying microbial systems have proved their utility as complements to the very powerful approaches regularly employed by electron microscopists. In addition, in recent geomicrobiological studies, researchers have begun to take advantage of the strengths of each technique by using the superior spatial resolution of the electron microscope (relative to the X-ray microscope) and the superior elemental sensitivity of the X-ray microscope (relative to the electron microscope), along with the ability of the X-ray microscope to spatially probe the chemical speciation of elements. The benefits of integrating these two nanoprobes for investigating the same microenvironments within a geomicrobial system are far superior to those of independent studies separately employing each probe. [source] Time-resolved structural studies of protein reaction dynamics: a smorgasbord of X-ray approachesACTA CRYSTALLOGRAPHICA SECTION A, Issue 2 2010Sebastian Westenhoff Proteins undergo conformational changes during their biological function. As such, a high-resolution structure of a protein's resting conformation provides a starting point for elucidating its reaction mechanism, but provides no direct information concerning the protein's conformational dynamics. Several X-ray methods have been developed to elucidate those conformational changes that occur during a protein's reaction, including time-resolved Laue diffraction and intermediate trapping studies on three-dimensional protein crystals, and time-resolved wide-angle X-ray scattering and X-ray absorption studies on proteins in the solution phase. This review emphasizes the scope and limitations of these complementary experimental approaches when seeking to understand protein conformational dynamics. These methods are illustrated using a limited set of examples including myoglobin and haemoglobin in complex with carbon monoxide, the simple light-driven proton pump bacteriorhodopsin, and the superoxide scavenger superoxide reductase. In conclusion, likely future developments of these methods at synchrotron X-ray sources and the potential impact of emerging X-ray free-electron laser facilities are speculated upon. [source] Cloning, expression, purification and preliminary X-ray crystallographic studies of Escherichia coli Hsp100 nucleotide-binding domain 2 (NBD2)ACTA CRYSTALLOGRAPHICA SECTION D, Issue 6-2 2002Jingzhi Li Escherichia coli Hsp100 ClpB has been identified recently as playing critical roles in multi-chaperone systems. ClpB binds and disaggregates denatured polypeptides by employing ATP hydrolysis and allows other molecular chaperones such as Hsp70 DnaK and Hsp40 DnaJ to refold the non-native polypeptides. ClpB contains two nucleotide-binding domains (NBD1 and NBD2) in its primary sequence. Walker A and Walker B motifs exist in both nucleotide-binding domains. Therefore, ClpB belongs to the large ATPase family known as ATPase associated with various cellular activities (AAA). The mechanisms by which NBD1 and NBD2 function to support the ClpB molecular-chaperone activity are currently unknown. To investigate how NBD2 participates in ClpB function to disaggregate denatured proteins, ClpB NBD2 has been cloned and crystallized. The ClpB NBD2 crystals diffract X-rays to 2.5,Å using synchrotron X-ray sources. The crystals belong to space group P212121, with unit-cell parameters a = 99.57, b = 149.34, c = 164.69,Å. [source] | ||||||||||