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339 citations found for Yamamoto,

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Acta Cryst. (2014). A70, C569
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X-ray irradiation on a protein crystal can cause some subtle structural modification on the protein structure even if the radiation dose is much smaller than a dose used for a common crystal structure determination. In some case such structural modification increases ambiguity of structural inspection, and eventually could be an obstacle on the elucidation of structure basis of protein function. Bovine heart cytochrome c oxidase (CcO) is one of such proteins having some problem caused by the radiation damage. The proton pumping of CcO is coupled with O2 reduction at the O2 reduction site, thus accurate structure determination of bound ligand as well as CcO itself is very important. Whereas accurate structure determination was impeded by the immediate photolysis of the peroxide ligand upon X-ray irradiation even at a cryogenic temperature[1]. We developed a goniometer based data collection system for the femtosecond crystallography at SACLA (SPring-8 Angstrom Compact free-electron LAser). The femtosecond crystallography is expected to have an advantage in high-resolution and radiation damage free structure determination of very large protein by combined usage of large crystal and femtosecond intense X-ray pulse. In this presentation we are going to show the result of the femtosecond crystallography on the crystal of CcO having large unit cell dimensions. The close inspection of the electron density map calculated at 1.9 Å resolution showed the femtosecond crystallography worked fine for the high resolution and radiation damage free crystal structure determination of CcO.


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An alkaline mannanase from a Bacillus sp. was crystallized and the crystals diffracted to 1.65 Å using synchrotron radiation. Phasing was successfully carried out using the molecular-replacement method.

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To characterize the defect sites in the near-surface and bulk phase of Li-MgO and Li-La2O3-MgO, XANES at Mg K-edge and La L3-edge was applied. For Li-MgO, it can be suggested that Li doping at a low content (2.5 wt%) brings about the formation of defect species only in the near-surface. This is due to the localization of doped Li ions in the surface, and thus the catalytically active species containing [Li+-O-] type center exist in the surface region. After OCM reaction, the defect species are formed in the near-surface over MgO and Li-MgO. By addition of La2O3 to Li-MgO (La/(Mg+La)=0.25), the structural change during the reaction is almost suppressed in the surface. In addition, the Li-La2O3-MgO shows higher C2 selectivity than Li-MgO.

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A new temperature-controllable humidifier for X-ray diffraction has been developed. It is shown that the humidifier can successfully maintain protein crystal growth at a temperature lower than room temperature.

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Advantages of using a wavelength of 2.7 Å over a wavelength of 1.9 Å for native single-wavelength anomalous dispersion phasing are presented, and potentials of using a wavelength of 3.3 Å are discussed.

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The oligomeric state of the 2-Cys peroxiredoxin from the green alga Chlamydomonas reinhardtii was determined by an X-ray crystallographic study and high-speed AFM image analysis.


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A new cassette system for protein cryocrystallography has been developed. This system is compatible with crystal-exchange robots installed at both SPring-8 and the Photon Factory.

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RIKEN beamline I (BL45XU) is an undulator beamline with two branches. One is for protein crystallography (PX) and the other is for small-angle x-ray scattering (SAXS). The beam is split into the two branches by a diamond monochromator so that two experiments can be done simultaneously [Yamamoto et al. (1995) Rev. Sci. Instrum. 66, 1833-1835]. The SAXS branch was designed for studying the weak interaction of proteins or subunits of fibrous or protein solutions especially using hydrostatic pressure. The optics makes use of the good parallelism of the undulator beam in order to reduce parasitic scattering. The beamline consists of a double crystal monochromator and a K-B type focusing mirror system. In order to cope with the high flux of the beam, an x-ray image intensifier (Hamamatsu Photonics, V5445P) with a cooled CCD camera (C4880-82) was used. As a result, decreases in both collection time and sample amount were realized in standard static experiments. These improvements will greatly facilitate SAXS experiments under high pressure.

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A highly stable, periodic approximant to Al-based F-type icosahedral quasicrystals, i-Al-Pd-TM (TM = transition metals), has been synthesized for the first time. A thorough investigation of the crystal structure leads to a universal description of a broader class of complex crystal structures closely related to the quasicrystals.

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Acta Cryst. (2011). A67, C631
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SPring-8 is constructing most of its beamlines by combination of standardized components according to the light-source characteristics. Specifications of components as well as a unified method of assembly and alignment are described.

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The observation of O2 in a time-frozen structure using serial femtosecond rotation crystallography of the as-isolated oxidized enzyme provides long-awaited clear-cut evidence for the mode of O2 binding in CuNiRs. This provides an insight into how CuNiR from A. xylosoxidans can function as an oxidase, reducing O2 to H2O2, or as a superoxide dismutase (SOD) since it was shown to have ∼56% of the dismutase activity of the bovine SOD enzyme some two decades ago.

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Damage-free structures of the resting state of one of the most studied copper nitrite reductases were obtained independently by X-ray free-electron laser (XFEL) and neutron crystallography, representing the first direct comparison of neutron and XFEL structural data for any protein. In addition, damage-free structures of the reduced and nitrite-bound forms have been obtained to high resolution from cryogenically maintained crystals by XFEL crystallography.

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Acta Cryst. (2017). A73, a343
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A shutterless continuous rotation method using an X-ray complementary metal-oxide semiconductor (CMOS) detector has been developed for high-speed, precise data collection in protein crystallography. The new method and detector were applied to the structure determination of three proteins by multi- and single-wavelength anomalous diffraction phasing and have thereby been proved to be applicable in protein crystallography.

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A new room-temperature (RT) data-collection method for microcrystals was developed by combining serial synchrotron rotation crystallography with the humid air and glue-coating method. The RT data-collection strategy for micro-crystallography was evaluated by examining the efficiency, the influence of non-isomorphism and radiation damage, and the effectiveness of increasing the number of merged images. An equation was proposed that relates the achievable resolution to the total photon flux used to obtain a data set.

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