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Photon Factory (photon + factory)
Selected AbstractsSymmetrization 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] Performance of a new furnace for high-resolution synchrotron powder diffraction up to 1900,K: application to determine electron density distribution of the cubic CaTiO3 perovskite at 1674,KJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 5 2004Masatomo Yashima Accurate crystal structure analysis at high temperatures is an important challenge in science and technology. A new electric furnace for the measurement of high-resolution (,d/d = 0.03%) synchrotron radiation powder diffraction profiles from materials at high temperatures (up to 1900,K in air) has been designed and fabricated. This furnace consists of a ceramic refractory with MoSi2 heaters, an aluminium body cooled by flowing water, and a sample stage with a spinner and a controller for sample-height adjustment. In situ synchrotron powder diffraction measurement for a calcium titanate perovskite specimen at 1674,K has been performed using the furnace at beamline 3A of the Photon Factory. The electron density distribution of the cubic perovskite at 1674,K was successfully obtained using a combination of Rietveld refinement, the maximum-entropy method (MEM) and MEM-based pattern-fitting techniques. The Ti atoms exhibit covalent bonding with the O atoms in the cubic CaTiO3 perovskite at this temperature, while the Ca atoms are ionic. These results indicate that the new furnace yields high-quality data for accurate crystal structure analysis. [source] Deconvolution of instrumental aberrations for synchrotron powder X-ray diffractometryJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2003T. Ida A method to remove the effects of instrumental aberrations from the whole powder diffraction pattern measured with a high-resolution synchrotron powder diffractometer is presented. Two types of asymmetry in the peak profiles caused by (i) the axial-divergence aberration of the diffractometer (diffractometer aberration) and (ii) the aberration of the monochromator and focusing optics on the beamline (beamline aberration) are both taken into account. The method is based on the whole-pattern deconvolution by Fourier technique combined with the abscissa-scale transformation appropriate for each instrumental aberration. The experimental powder diffraction data of LaB6 (NIST SRM660) measured on beamline BL-4B2 at the Photon Factory in Tsukuba have been analysed by the method. The formula of the scale transformation for the diffractometer aberration has a priori been derived from the instrumental function with geometric parameters of the optics. The strongly deformed experimental peak profiles at low diffraction angles have been transformed to sharp peak profiles with less asymmetry by the deconvolution of the diffractometer aberration. The peak profiles obtained by the deconvolution of the diffractometer aberration were modelled by an asymmetric model profile function synthesized by the convolution of the extended pseudo-Voigt function and an asymmetric component function with an empirical asymmetry parameter, which were linearly dependent on the diffraction angle. Fairly symmetric peak profiles have been obtained by further deconvolution of the empirically determined asymmetric component of the beamline aberration. [source] Implementation of remote monitoring and diffraction evaluation systems at the Photon Factory macromolecular crystallography beamlinesJOURNAL OF SYNCHROTRON RADIATION, Issue 3 2008Yusuke Yamada Owing to recent advances in high-throughput technology in macromolecular crystallography beamlines, such as high-brilliant X-ray sources, high-speed readout detectors and robotics, the number of samples that can be examined in a single visit to the beamline has increased dramatically. In order to make these experiments more efficient, two functions, remote monitoring and diffraction image evaluation, have been implemented in the macromolecular crystallography beamlines at the Photon Factory (PF). Remote monitoring allows scientists to participate in the experiment by watching from their laboratories, without having to come to the beamline. Diffraction image evaluation makes experiments easier, especially when using the sample exchange robot. To implement these two functions, two independent clients have been developed that work specifically for remote monitoring and diffraction image evaluation. In the macromolecular crystallography beamlines at PF, beamline control is performed using STARS (simple transmission and retrieval system). The system adopts a client,server style in which client programs communicate with each other through a server process using the STARS protocol. This is an advantage of the extension of the system; implementation of these new functions required few modifications of the existing system. [source] High-throughput operation of sample-exchange robots with double tongs at the Photon Factory beamlinesJOURNAL OF SYNCHROTRON RADIATION, Issue 3 2008Masahiko Hiraki Sample-exchange robots that can exchange cryo-pins bearing protein crystals out of experimental hutches according to user instructions have been developed. The robots were designed based on the SAM (Stanford Synchrotron Research Laboratory automated mounting) system. In order to reduce the time required for the sample exchange, the single tongs of the SAM system were modified and a double-tongs system that can hold two cryo-pins at the same time was developed. Robots with double tongs can move to the goniometer head holding the next cryo-pin with one set of tongs, dismount the experimented cryo-pin with the other set, and then mount the next pin onto the goniometer head without leaving the diffractometer area. Two different types of tongs have been installed: single tongs at beamlines BL-5A and AR-NW12A, and a double-tongs system at beamline BL-17A of the Photon Factory. The same graphical user interface software for operation of the sample-exchange robots is used at all beamlines, however, so that users do not need to consider differences between the systems. In a trial, the robot with double tongs could exchange samples within 10,s. [source] Developing 100,ps-resolved X-ray structural analysis capabilities on beamline NW14A at the Photon Factory Advanced RingJOURNAL OF SYNCHROTRON RADIATION, Issue 4 2007Shunsuke Nozawa NW14A is a newly constructed undulator beamline for 100,ps time-resolved X-ray experiments at the Photon Factory Advanced Ring. This beamline was designed to conduct a wide variety of time-resolved X-ray measurements, such as time-resolved diffraction, scattering and X-ray absorption fine structure. Its versatility is allowed by various instruments, including two undulators, three diffractometers, two pulse laser systems and an X-ray chopper. The potential for the detection of structural changes on the 100,ps time scale at NW14A is demonstrated by two examples of photo-induced structural changes in an organic crystal and photodissociation in solution. [source] Changes at Photon Factory and KEKJOURNAL OF SYNCHROTRON RADIATION, Issue 2 2003DOI: 10.1107/S090904950300310 First page of article [source] Large-area phase-contrast X-ray imaging using a two-crystal X-ray interferometerJOURNAL OF SYNCHROTRON RADIATION, Issue 5 2002Akio Yoneyama Large-area (25,×,20,mm) phase-contrast X-ray imaging was attained by using a skew-symmetric two-crystal X-ray interferometer. The sub-nrad angular control required to operate the X-ray interferometer was achieved with a sleeve bearing and a feedback-positioning system. As a demonstration, measurements of a phase map of a rat's liver and a phase-contrast tomographic three-dimensional image of a piece of a rabbit's liver were performed at the Photon Factory using 0.07,nm synchrotron radiation X-rays. [source] Zernike-type phase-contrast hard X-ray microscope with a zone plate at the Photon FactoryJOURNAL OF SYNCHROTRON RADIATION, Issue 3 2002Hiroki Yokosuka A Zernike-type phase-contrast X-ray microscope with a zone plate and a phase plate was constructed at the Photon Factory BL3C2. Parallel monochromatic X-rays of 8.97,keV were incident on a specimen and a direct beam transmitted through the specimen was focused on the back focal plane of the zone plate, where an aluminium phase plate was placed. Tantalum line patterns as fine as 0.3,µm could be imaged. Phase-contrast images of polypropylene wires and polystyrene latex beads were obtained, which showed better contrast than that of their bright field images. [source] Expression, crystallization and preliminary X-ray crystallographic studies of Arthrobacter globiformis inulin fructotransferaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2003Mitsuru Momma A recombinant form of Arthrobacter globiformis inulin fructotransferase (DFAIII-producing) has been overexpressed in Escherichia coli and purified to homogeneity. Crystals were obtained at 293,K by the hanging-drop vapour-diffusion technique using 0.1,M Na HEPES pH 7.5 buffer containing 1.5,M lithium sulfate as a precipitant. Crystals of the recombinant wild-type enzyme diffracted to better than 1.5,Å at 100,K using a synchrotron-radiation source at the Photon Factory. The crystal belonged to space group R32, with unit-cell parameters a = b = 92.02, c = 229.82,Å in the hexagonal axes. Assuming the presence of one molecule in the asymmetric unit, the VM value for the crystal was 2.15,Å3,Da,1, indicating a solvent content of 42.8%. Selenomethionine-derivative crystals belonged to a different space group, C2, with unit-cell parameters a = 159.32, b = 91.92, c = 92.58,Å, , = 125.06. Matthews coefficient calculations suggested that the C2 selenomethionine-derivative crystal contained three molecules per asymmetric unit. [source] Crystallization and preliminary X-ray diffraction analysis of glutamate dehydrogenase from an aerobic hyperthermophilic archaeon, Aeropyrum pernix K1ACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2002Mohammad W. Bhuiya Glutamate dehydrogenase from an aerobic hyperthermophilic archaeon, Aeropyrum pernix K1, was crystallized by the hanging-drop vapour-diffusion method using polyethylene glycol (PEG) 400 as the precipitant. The crystals belong to the hexagonal space group P63, with unit-cell parameters a = b = 98.9, c = 394.8,Å, , = , = 90, , = 120°. The asymmetric unit contained one hexamer of the enzyme, giving a crystal volume per enzyme mass (VM) of 1.98,Å3,Da,1 and a solvent content of 37.3%. The X-ray diffraction data were collected to a resolution of 3.0,Å at the BL6B beamline in the Photon Factory with an overall Rsym of 13.8% and a completeness of 87.1%. [source] Preliminary X-ray crystallographic analysis of SMU.2055 protein from the caries pathogen Streptococcus mutansACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2010Wang-Hong Zhao The SMU.2055 gene from the major caries pathogen Streptococcus mutans is annotated as a putative acetyltransferase with 163 amino-acid residues. In order to identify its function via structural studies, the SMU.2055 gene was cloned into the expression vector pET28a. Native and SeMet-labelled SMU.2055 proteins with a His6 tag at the N-terminus were expressed at a high level in Escherichia coli strain BL21 (DE3) and purified to homogeneity by Ni2+ -chelating affinity chromatography. Diffraction-quality crystals of SeMet-labelled SMU.2055 were obtained using the sitting-drop vapour-diffusion method and diffracted to a resolution of 2.5,Å on beamline BL17A at the Photon Factory, Tsukuba, Japan. The crystals belong to the orthorhombic space group C2221, with unit-cell parameters a = 92.0, b = 95.0, c = 192.2,Å. The asymmetric unit contained four molecules, with a solvent content of 57.1%. [source] Crystallization and preliminary X-ray analysis of a monomeric mutant of Azami-Green (mAG), an Aequorea victoria green fluorescent protein-like green-emitting fluorescent protein from the stony coral Galaxea fascicularisACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 12 2009Tatsuki Ebisawa Monomeric Azami-Green (mAG) from the stony coral Galaxea fascicularis is the first monomeric green-emitting fluorescent protein that is not a derivative of Aequorea victoria green fluorescent protein (avGFP). mAG and avGFP are 27% identical in amino-acid sequence. Diffraction-quality crystals of recombinant mAG were obtained by the sitting-drop vapour-diffusion method using PEG 3350 as the precipitant. The mAG crystal diffracted X-rays to 2.20,Å resolution on beamline AR-NW12A at the Photon Factory (Tsukuba, Japan). The crystal belonged to space group P1, with unit-cell parameters a = 41.78, b = 51.72, c = 52.89,Å, , = 90.96, , = 103.41, , = 101.79°. The Matthews coefficient (VM = 2.10,Å3,Da,1) indicated that the crystal contained two mAG molecules per asymmetric unit. [source] Crystallization and preliminary X-ray characterization of a PaaX-like protein from Sulfolobus solfataricus P2ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2009Yi Cao PaaX is a global regulator of the phenylacetyl-coenzyme A catabolon that adjusts the expression of different operons to that of the paa -encoded central pathway. In this study, the PaaX-like protein from the hyperthermophilic archaeon Sulfolobus solfataricus P2 was successfully crystallized by the hanging-drop vapour-diffusion method using ammonium sulfate as a precipitant. Diffraction data were obtained to a resolution of 3.0,Å using synchrotron radiation at the Photon Factory. The crystal belonged to space group P321, with unit-cell parameters a = 86.4, b = 86.4, c = 105.5,Å. [source] Crystallization and preliminary X-ray diffraction analysis of the tRNA-modification enzyme GidA from Aquifex aeolicusACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2009Takuo Osawa The 5-carboxymethylaminomethyl modification of uridine at the first position of the tRNA anticodon is crucial for accurate protein synthesis by stabilizing the correct codon,anticodon pairing on the ribosome. Two conserved enzymes, GidA and MnmE, are involved in this modification process. Aquifex aeolicus GidA was crystallized in two different crystal forms: forms I and II. These crystals diffracted to 3.2 and 2.3,Å resolution, respectively, using synchrotron radiation at the Photon Factory. These crystals belonged to space groups I212121 and P21 with unit-cell parameters a = 101.6, b = 213.3, c = 231.7,Å and a = 119.4, b = 98.0, c = 129.6,Å, , = 90.002°, respectively. The asymmetric units of these crystals are expected to contain two and four molecules, respectively. [source] Crystallization and preliminary X-ray crystallographic analysis of SMU.412c protein from the caries pathogen Streptococcus mutansACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2009Zhao-Yang Ye The smu.412c gene encodes a putative histidine triad-like protein (SMU.412c) with 139 residues that is involved in cell-cycle regulation in Streptococcus mutans. The gene was cloned into the expression vector pET28a and subsequently expressed in Escherichia coli strain BL21 (DE3) to give a substantially soluble form of SMU.412c with a His6 tag at its N-terminus. The recombinant protein was purified to homogeneity in a two-step procedure involving Ni2+ -chelating and size-exclusion chromatography. Crystals suitable for X-ray diffraction were obtained using the sitting-drop vapour-diffusion method and diffracted to 1.8,Å resolution on beamline BL6A at Photon Factory, Tsukuba, Japan. The crystal belonged to space group P41212, with unit-cell parameters a = b = 53.5, c = 141.1,Å. [source] Crystallization and X-ray diffraction analysis of the RNA primer/promoter-binding domain of influenza A virus RNA-dependent RNA polymerase PB2ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 2 2009Takashi Kuzuhara The C-terminal domain protein (amino-acid residues 535,759) of the PB2 subunit of the RNA-dependent RNA polymerase from the highly pathogenic influenza A virus was expressed as a soluble protein in Escherichia coli and crystallized using sodium formate as a precipitant. Data sets were collected from crystals of native and selenomethionine-substituted protein on the KEK NW12 beamline at the Photon Factory and the crystals diffracted to a maximum resolution of 2.44,Å for the SeMet-derivative crystal. The native crystals were found to belong to space group P3221, with unit-cell parameters a = b = 52.5, c = 156.3,Å. The Matthews value (VM) was 2.7,Å3,Da,1, assuming the presence of one molecule in the asymmetric unit. The SeMet-derivative crystals were found to belong to the same space group, with unit-cell parameters a = b = 52.6, c = 156.4,Å. Attempts are being made to solve the structure by multi-wavelength anomalous dispersion phasing. [source] Crystallization and preliminary X-ray studies of the chromophore-binding domain of cyanobacteriochrome AnPixJ from Anabaena sp.ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 2 2009PCC 7120 Cyanobacteriochromes form a recently defined superfamily of tetrapyrrole-based photoreceptors that are distantly related to conventional red/far-red photoreceptor phytochromes. Among these molecules, AnPixJ from Anabaena sp. PCC 7120 is a novel photoreceptor that shows reversible photoconversion between green-absorbing and red-absorbing forms, which is in contrast to the properties of conventional phytochromes. In order to better understand the structural basis of this unique photoconversion mechanism, the chromophore-binding domain of AnPixJ (AnPixJ-GAF2) was heterologously overproduced and purified, and crystallization of both forms was attempted. Blue crystals of the red-absorbing form of AnPixJ-GAF2 were successfully obtained; they belonged to space group P43212 and contained one monomer per asymmetric unit. Diffraction data were collected to a resolution of 1.8,Å using synchrotron-radiation beamline BL-5A at the Photon Factory. [source] Crystallization and X-ray analysis of 2-deoxy- scyllo -inosose synthase, the key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibioticsACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2005Eriko Nango A recombinant 2-deoxy- scyllo -inosose synthase from Bacillus circulans has been crystallized at 277,K using PEG 4000 as precipitant. The diffraction pattern of the crystal extends to 2.30,Å resolution at 100,K using synchrotron radiation at the Photon Factory. The crystals are monoclinic and belong to space group P21, with unit-cell parameters a = 80.5, b = 70.4, c = 83.0,Å, , = 117.8°. The presence of two molecules per asymmetric unit gives a crystal volume per protein weight (VM) of 2.89,Å3,Da,1 and a solvent constant of 57.4% by volume. [source] | ||||||||||