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Synchrotron Facility (synchrotron + facility)
Selected AbstractsCrystallization and preliminary X-ray analysis of Borrelia burgdorferi outer surface protein C (OspC)ACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2001D. Kumaran Single crystals of the outer surface protein C (OspC) from Borrelia burgdorferi HB19 have been obtained by the vapor-diffusion method. These crystals belong to space group P21, with unit-cell parameters a = 66.218, b = 46.113, c = 112.079,Å, , = 99.30°, and diffract to at least 2.2,Å resolution. Native data have been collected from flash-frozen crystals at the National Synchrotron facility of Brookhaven National Laboratory. There are two dimers per asymmetric unit, related by a non-crystallographic twofold axis and a pseudo-translational symmetry. [source] Crystallization and preliminary X-ray analysis of Clostridium botulinum neurotoxin type BACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2000S. Swaminathan Single crystals of Clostridium botulinum neurotoxin type B have been obtained by the vapor-diffusion method. These crystals belong to space group P21, with unit-cell parameters a = 76.08, b = 123.11, c = 95.86,Å, , = 113.03° and diffract to at least 1.8,Å resolution. Native data have been collected from flash-frozen crystals at the National Synchrotron facility of Brookhaven National Laboratory. These crystals often tend to be non-isomorphic. [source] The Beamline X28C of the Center for Synchrotron Biosciences: a National Resource for Biomolecular Structure and Dynamics Experiments Using Synchrotron FootprintingJOURNAL OF SYNCHROTRON RADIATION, Issue 3 2007Sayan Gupta Structural mapping of proteins and nucleic acids with high resolution in solution is of critical importance for understanding their biological function. A wide range of footprinting technologies have been developed over the last ten years to address this need. Beamline X28C, a white-beam X-ray source at the National Synchrotron Light Source of Brookhaven National Laboratory, functions as a platform for synchrotron footprinting research and further technology development in this growing field. An expanding set of user groups utilize this national resource funded by the National Institute of Biomedical Imaging and Bioengineering of the National Institutes of Health. The facility is operated by the Center for Synchrotron Biosciences and the Center for Proteomics of Case Western Reserve University. The facility includes instrumentation suitable for conducting both steady-state and millisecond time-resolved footprinting experiments based on the production of hydroxyl radicals by X-rays. Footprinting studies of nucleic acids are routinely conducted with X-ray exposures of tens of milliseconds, which include studies of nucleic acid folding and their interactions with proteins. This technology can also be used to study protein structure and dynamics in solution as well as protein,protein interactions in large macromolecular complexes. This article provides an overview of the X28C beamline technology and defines protocols for its adoption at other synchrotron facilities. Lastly, several examples of published results provide illustrations of the kinds of experiments likely to be successful using these approaches. [source] Performance limits of direct cryogenically cooled silicon monochromators , experimental results at the APSJOURNAL OF SYNCHROTRON RADIATION, Issue 1 2000Wah-Keat Lee The successful use of cryogenically cooled silicon monochromators at third-generation synchrotron facilities is well documented. At the Advanced Photon Source (APS) it has been shown that, at 100,mA operation with the standard APS undulator A, the cryogenically cooled silicon monochromator performs very well with minimal (<2 arcsec) or no observable thermal distortions. However, to date there has not been any systematic experimental study on the performance limits of this approach. This paper presents experimental results on the performance limits of these directly cooled crystals. The results show that if the beam is limited to the size of the radiation central cone then, at the APS, the crystal will still perform well at twice the present 100,mA single 2.4,m-long 3.3,cm-period undulator heat load. However, the performance would degrade rapidly if a much larger incident white-beam size is utilized. [source] Bulk mineralogy and three-dimensional structures of individual Stardust particles deduced from synchrotron X-ray diffraction and microtomography analysisMETEORITICS & PLANETARY SCIENCE, Issue 1-2 2008Tomoki Nakamura The analyses were performed at synchrotron facilities, KEK and SPring-8 in Japan. Twenty-eight particles from 5 to 25 ,m in size, including 25 particles from Track 35 and 3 particles from Track 44, were first analyzed by X-ray diffraction and then 4 out of 28 particles were analyzed by X-ray tomography. All particles are classified into two groups based on silicate crystallinity: crystalline type and amorphous-rich type. The abundance of the former is approximately 10% of the particles investigated. Crystalline type shows very sharp reflections of olivine and low-Ca pyroxene, while amorphous-rich type shows no or very weak silicate reflections, suggesting that silicates are mostly amorphous. Broad reflections of Fe sulfides and Fe silicides are detected from most of amorphous-rich type particles. Subsequent tomography analysis revealed that the crystalline type is non-porous material consisting of coarse silicate crystals larger than 1 ,m in size, while the amorphous-rich type is very porous aggregates with amorphous silicates and small Fe sulfide and Fe metallic grains. All characteristics of amorphous-rich type particles indicate that most of them are melted and rapidly solidified during capture in the silica aerogel. On the other hand, the crystalline type is indigenous cometary particle formed through high-temperature heating episodes that have taken place prior to formation of comet Wild 2. One of the crystalline-type particles (C2054,0,35,6,0) consists of Mg-rich olivine, pyroxene, and kamacite and exhibits porphyritic or poikilitic texture very similar to chondrules. [source] Crystallization and preliminary X-ray diffraction studies of the water-soluble state of the pore-forming toxin sticholysin II from the sea anemone Stichodactyla helianthusACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2002José M. Mancheño Sticholysin II (StnII) is a potent cytolytic protein produced by the sea anemone Stichodactyla helianthus. StnII belongs to the actinoporin family, a group of proteins which are characterized by their ability to spontaneously interact with biological membranes. The cytolytic character of these proteins is currently explained in terms of a molecular mechanism involving the formation of transmembrane pores. StnII has been crystallized using the hanging-drop vapour-diffusion method at 291,K. Diffraction-quality crystals have unit-cell parameters a = 32.30, b = 119.73, c = 43.42,Å, , = 90.04° and belong to the monoclinic space group P21. Diffraction data to a resolution of 1.71,Å were collected at synchrotron facilities. [source] Negative (and very low) thermal expansion in ReO3 from 5 to 300,KJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2009Monica Dapiaggi This paper reports the accurate measurement of the ReO3 cell parameter as a function of temperature. The thermal expansion is confirmed to be negative over most of the temperature range from 5 to 300,K. The main problems with the measurements are the very small variations (in the range of 10,5,Å) in the cell parameter at each temperature, requiring tight control of the stability and reliability of instrumental effects. In particular, achieving monochromator stability over time might be challenging with the high energy and high beam current variations of a third-generation synchrotron facility. On the other hand, such effects are usually checked by the addition of silicon as an internal standard, but the accuracy (and precision) of the published thermal expansion (which is not certified) might not be sufficient for its use when dealing with very small cell parameter variations. [source] Symmetrization of diffraction peak profiles measured with a high-resolution synchrotron X-ray powder diffractometerJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 1 2006H. Hibino The asymmetry of diffraction peak profiles observed with a high-resolution synchrotron powder X-ray diffractometer has been successfully removed by a double deconvolution method. In the first step, the asymmetry caused by the axial divergence aberration of the diffractometer is removed by a whole-pattern deconvolution method based on an a priori theoretical model for the aberration. In the second step, the residual asymmetry, the origin of which can be ascribed to the aberrations of the beamline optics, is also removed by a whole-pattern deconvolution method, based on an empirical model derived from the analysis of experimental diffraction peak profiles of a standard Si powder (NIST SRM640b). The beamline aberration has been modelled by the convolution of a pseudo-Voigt or Voigt function with an exponential distribution function. It has been found that the angular dependence of the asymmetry parameter in the exponential function is almost proportional to tan,, which supports the idea that the residual asymmetry should be ascribed mainly to the intrinsic asymmetry in the spectroscopic distribution of the source X-ray supplied by the beamline optics of the synchrotron facility. Recently developed procedures of whole-pattern deconvolution have been improved to treat the singularity of the instrumental function in the measured angular range. Formulae for the whole-pattern deconvolution based on the Williamson,Hall-type dependence of the width parameter of the instrumental function have also been developed. The method was applied to the diffraction intensity data of a standard ZnO powder sample (NIST SRM674) measured with a high-resolution powder diffractometer on beamline BL4B2 at the Photon Factory. The structure parameters of ZnO were refined from the integrated peak intensities, which were extracted by an individual profile fitting method applying symmetric profile models. The refined structure parameters coincide fairly well with those obtained from single-crystal data. [source] In-situ IR synchrotron mapping ellipsometry on stimuli-responsive PAA-b-PS/PEG mixed polymer brushesPHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 2 2010Dennis Aulich Abstract A binary polymer brush consisting of weak polyelectrolytes was investigated with infrared synchrotron mapping ellipsometry in-situ under the influence of different aqueous solutions. Thickness of the brush layer in dry state was ,15 nm. The brush, consisting of poly(ethylene glycol) and poly(acrylic acid)-b-poly(styrene) in a 50/50 composition was switched between two different states by changing the pH of the solution. An IR mapping ellipsometer at the IRIS beamline located at the BESSY II synchrotron facility in Berlin, Germany, was used for high lateral resolution in-situ measurements. The results show strong chemical changes in the brush layer due to COOH , COO, conversion of the PAA's carboxylic groups. Measurements with spot sizes of ,1 mm on different positions on the samples proved good homogeneity of the brush layer and the qualification of this method for investigation of ultrathin organic films in aqueous solutions in-situ with IR ellipsometry. (© 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Expression, refolding, crystallization and preliminary crystallographic study of MHC H-2Kk complexed with octapeptides and nonapeptidesACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2004Christine Kellenberger Major histocompatibility complex (MHC) molecules are heterodimeric cell-surface receptors that play a crucial role in the cellular immune response by presenting epitope peptides to T-cell antigen receptors (TCR). Although the structural basis of the peptide,MHC binding mechanism is becoming better understood, it is still difficult to predict a binding mode for an MHC of unknown structure. Therefore, as the first stage of a TCR,MHC interaction study, the crystal structures of the mouse H-2Kk molecule in complex with both an octapeptide from Influenza A virus and a nonapeptide from simian virus SV40 were solved. Here, the expression, refolding, purification and crystallization of the two complexes are reported. For the H-2Kk,HA(259,266) complex, crystals were obtained via an extensive screen using a nanodrop-dispensing robot and diffracted to 2.5,Å resolution. For the H-2Kk,SV40(560,568) complex, microscopic needles were initially obtained and their size was improved by macroseeding and a stepwise increase in precipitant concentration. Diffraction data to a resolution of 3.0,Å were collected at a synchrotron facility. [source] Structure of HsaD, a steroid-degrading hydrolase, from Mycobacterium tuberculosisACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 1 2008Nathan Lack Tuberculosis is a major cause of death worldwide. Understanding of the pathogenicity of Mycobacterium tuberculosis has been advanced by gene analysis and has led to the identification of genes that are important for intracellular survival in macrophages. One of these genes encodes HsaD, a meta -cleavage product (MCP) hydrolase that catalyzes the hydrolytic cleavage of a carbon,carbon bond in cholesterol metabolism. This paper describes the production of HsaD as a recombinant protein and, following crystallization, the determination of its three-dimensional structure to 2.35,Å resolution by X-ray crystallography at the Diamond Light Source in Oxfordshire, England. To the authors' knowledge, this study constitutes the first report of a structure determined at the new synchrotron facility. The volume of the active-site cleft of the HsaD enzyme is more than double the corresponding active-site volumes of related MCP hydrolases involved in the catabolism of aromatic compounds, consistent with the specificity of HsaD for steroids such as cholesterol. Knowledge of the structure of the enzyme facilitates the design of inhibitors. [source] | |||||||||||||