Application of the two-dimensional detectors, IP and CCD detectors, to chemical crystallography is advantageous for accurate and fast intensity measurements, and easy and quick observations of two-dimensional diffraction images. 2D detectors are very useful for structural studies of the phase transition phenomena in which diffuse scattering and/or superlattice reflections are observed, time-resolved X-ray structure analyses of the photo-excited species and the photoinduced reactive species, and also micro-crystal structure analyses.
Optics development for synchrotron hard X-rays carried out at the SPring-8 is reviewed. Included are (i) optics and beamline standardization for the SPring-8 and (ii) coherence-related optics most recently carried out at the SPring-8.
Atom-resolved holography has been developed in the last two decade. Based on X-ray holography, its principle is described briefly and quality of atomic images depending on the cluster size and reconstruction techniques is discussed. Furthermore, πXAFS, γ and neutron holography are introduced.
To understand the catalytic mechanism of an enzyme, it is crucial to determine the crystallographic structures corresponding to the individual reaction steps. Here we report two crystal structures of enzyme-substrates complexes prior to reaction initiation : tropinone reductase-II (TR-II) -NADPH and TR-II-NADPH-tropinone complexes, determined from the identical crystals. A combination of two kinetic crystallographic techniques, a continuous flow of the substrates and Laue diffraction measurement, enabled us to capture the transit structures prior to the reaction proceeding. A structure comparison of enzyme-substrates complex elucidated in this study with the enzyme-products complex in our previous study indicates that one of the substrates, tropinone, is rotated relative to the product so as to make the spatial organization in the active site favorable for the reaction to proceed. Side chains of the residues in the active site also alter their conformations to keep the complementarily of the space for the substrate or the product and to assist the rotational movement.
A real-space imaging of a local thermal vibration anomaly in a solid has been demonstrated for the first time, through atomic-resolution annular dark-field scanning transmission electron microscope (ADF-STEM) observations of an Al72Ni20Co8 quasicrystalline compound. Significant changes of ADF-contrast depending on the observation temperature as well as the scattering angle ranges are found to be obvious at some particular Al atomic sites. The origin of this anomalous ADF-contrast is explained fairly well by the thermal diffuse scattering (TDS) intensity change due to different values of temperature (Debye-Waller) factor, which is defined by mean-square thermal vibration amplitude of the atoms.
The crystal structure of natural Diels-Alderase, macrophomate synthase, in complex with pyruvate was determined at 1.7 Å resolution. The structure explains broad substrate specificity and provides mechanistic information regarding the multiple catalyst of this enzyme. The active site reveals several ingenious features for catalyzing the Diels-Alder reaction, which include the existence of residues for making catalytically important hydrogen bonds to the 2-pyrone. The rather large and hydrophobic milieu in the active site cavity allows a large-scale structural reorganization of the product imposed to escape product inhibition. These findings are useful for understanding the strategy of a natural Diels-Alderase, which have been acquired during a long time evolution.
A program to draw and analyze Kikuchi patterns is introduced, especially for electron back-scattering diffraction (EBSD) analysis that has become popular recently. The functions of the program include geometrical drawing of Kikuchi patterns with contrast from kinematical calculation, indexing of observed patterns, acquisition of camera parameters, etc. except for automated crystal orientation map measurement for polycrystalline materials. The program is available from an Internet website and performed on a Windows machine. The outline of the calculation methods in the program is described briefly.