Application of the Debye model to the temperature dependence of atomic mean square displacements determined by X-ray diffraction provides individual knowledge of dynamic and static natures of atomic displacements, together with characteristic values of crystals such as Debye temperature and one particle potential coefficients. The anharmonic refinement, incorporating the higher-order terms into the Debye-Waller factor, is a useful technique to detect the deformation of the probability density functions from ellipsoidal distribution due to anharmonic thermal vibrations and static disorders of atoms. Here we review our recent research that applied these approaches to Mg3Al2Si3O12 garnet, an important constituent in the Earth's interior. The research has proved the presence of the Mg static disorder, which has long been a controversial issue, and has proposed the possibility of anharmonic thermal vibrations of atoms at high temperature.
Resonant X-ray scattering techniques were applied for crystal-structure analyses for determining the valence state, charge ordering and magnetic structures in various minerals and inorganic compounds. The article includes the topics on absorption edge, Kramers-Kronig relation, anomalous scattering factors, two-wavelengths anomalous dispersion method, valence-difference contrast method, resonant scattering in electronic transition and resonant X-ray magnetic scattering.
History of the study of the Earth's deep interior was reviewed. In order to understand Earth's deep interior from the view point of materials science, X-ray diffraction under high pressure and high temperature played very important role. Use of synchrotron radiation dramatically advanced this experimental technique and it is now possible to make precise X-ray study under the P-T conditions corresponding even to the center of the Earth. In order to clarify the behavior of light elements such as hydrogen, however, studies using neutron diffraction are also required. A new neutron beam line dedicated for high-pressure science is constructed at J-PARC and is now ready for use.
Features of the three-dimensional (3D) visualization software VESTA and a program for maximum entropy method (MEM) analysis Dysnomia are reviewed. VESTA has a unique feature to simultaneously visualize crystal, volumetric and morphology data. Multiple numbers of crystal structure data can be overlaid and compared in the same 3D space. Two examples of how these features are utilized in the X-ray crystallographic study are presented. In Dysnomia, several new features are implemented for improvement of the results of MEM analysis and better performance of calculation. New features in the latest version of VESTA are also explained, and some thoughts on the future of crystallographic visualization software are discussed.
Bizen stoneware, with the characteristic reddish hidasuki or “fire-marked” pattern, is one of Japan's best known traditional ceramic works of art. We investigated the microstructure and color-formation process in Bizen stoneware, and discovered that the hidasuki pattern resulted from the precipitation of corundum (α-Al2O3) and the subsequent epitaxial growth of hematite (α-Fe2O3) around it in a ～50 µm-thick liquid specifically formed in the ceramic surface. The epitaxial composites include hexagonal plate-like α-Fe2O3/α-Al2O3/α-Fe2O3 sandwiched particles. At low oxygen partial pressures, α-Fe coated graphite, Fe3P and ε-Fe2O3 were also formed to appear.
Selenocysteine (Sec) is the 21st amino acid that is incorporated into proteins translationally. The selenocysteine tRNA (tRNASec) is first ligated with serine by seryl-tRNA synthetase, and the Ser moiety is converted to Sec in a tRNA-dependent manner. In Bacteria, the selenocysteine synthase SelA converts Ser to Sec directly, whereas in Eukaryotes and Archaea, phosphorylation of the Ser moiety is required prior to the Sec conversion. In this review, we describe the crystal structures of SelA, bacterial tRNASec, and the SelA•tRNASec complex. Based on the crystal structures and mutational analyses, the substrate discrimination and reaction mechanisms are discussed.
A novel protein crystal mounting method was developed using controlled humid air and hydrophobic polymer glue for crystal coating. The glue-coated crystals under the optimized humid air were quite stable at room temperature and could be cryocooled. This method is particularly useful when applied to fragile protein crystals known to be sensitive to environmental change. And, the crystals by using HAG method reproducibly showed crystal lattice transformation in response to a change in humidity, thus using this method a series of isomorphic crystals can be prepared.
Chitinase C from a moderate thermophilic strain Ralstonia sp. A-471 (Ra-ChiC) is a novel chitinase which has a catalytic domain sequence similar to goose type lysozymes and, unlike other chitinases, Ra-ChiC belongs to glycoside hydrolase family 23. We have determined the crystal structures of Ra-ChiC catalytic domain and its inactive mutant with or without chitin oligosaccharides. These structures indicated that Ra-ChiC has a unique substrate-binding site including a tunnel-shaped cavity. In addition, our mutation analysis showed that not only a highly conserved Glu141 but also Asp226 located at the roof of the tunnel have quite important roles in catalysis.