Nihon Kessho Gakkaishi
Online ISSN : 1884-5576
Print ISSN : 0369-4585
ISSN-L : 0369-4585
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Volume 57, Issue 5
Displaying 1-12 of 12 articles from this issue
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How Crystallography Plays Important Roles in Industries ?
  • Polarity Determination of GaN Thin Films by Anomalous X-Ray Diffraction
    Koichi AKIMOTO
    2015 Volume 57 Issue 5 Pages 263-268
    Published: October 31, 2015
    Released on J-STAGE: October 31, 2015
    DOIhttps://doi.org/10.5940/jcrsj.57.263
    JOURNAL FREE ACCESS
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    Recently, the wide bandgap semiconductor GaN and its alloys have been interested because of their superb properties for the fabrication of blue- or ultraviolet-light emitting devices. There is much interest in growth mechanism and the reduction of defects. The reported crystallographic structure of the GaN film is usually wurtzite or zinc blend type. Because the most common growth direction of the GaN film is normal to the {0001} plane of the wurtzite structure, it is very important to determine the polarity of the film. We determined the polarity of the GaN thin films grown on sapphire substrates by using anomalous X-ray diffraction techniques.
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Introduction and Practice of Crystal Structure Refinement Using SHELXL-2014
  • Let's Use SHELXL against Merohedral Twinning !
    Mao MINOURA
    2015 Volume 57 Issue 5 Pages 269-275
    Published: October 31, 2015
    Released on J-STAGE: October 31, 2015
    DOIhttps://doi.org/10.5940/jcrsj.57.269
    JOURNAL FREE ACCESS
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    In this tutorial course of SHELXL, we will focus on how to treat the twinning by merohedry. Merohedral twinning is not apparent during the measurement or in the diffraction pattern, and therefore, unsolved twinning and fuzzy molecular structures remain in the data folder. We would like to show the avoidable pitfalls that are to be considered for the correct molecular structures using examples of solved merohedral twin crystals and step by step tutorials for organ(ometall)ic chemists.
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Articles
  • Three-Dimensional Observation of Lattice Defects Using Electron Tomography
    Satoshi HATA, Masatoshi MITSUHARA, Hideharu NAKASHIMA, Ken-ichi IKEDA, ...
    2015 Volume 57 Issue 5 Pages 276-284
    Published: October 31, 2015
    Released on J-STAGE: October 31, 2015
    DOIhttps://doi.org/10.5940/jcrsj.57.276
    JOURNAL FREE ACCESS
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    Three-dimensionalization, i.e., direct representation or fabrication of three-dimensional (3D) objects, is now a key technology in various science and engineering fields. Electron microscopy, a vital nanoscale characterization tool, is no exception, thus various imaging methods have been developed to extend its imaging capabilities from conventional two dimensions to three dimensions. In this article, we focus on electron tomography (ET), which is a typical 3D imaging method using transmission electron microscopy (TEM) or scanning transmission electron microscopy（STEM）, and overview the current status and future prospects of ET and an application of ET to 3D imaging of dislocations in crystalline materials as an practical example.
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Articles
  • Raman Tensor Analysis by Angle-Resolved Polarized Spectroscopy
    Yasuhiro FUJII, Akitoshi KOREEDA, Takao SHIMIZU, Hiroki TANIGUCHI
    2015 Volume 57 Issue 5 Pages 285-290
    Published: October 31, 2015
    Released on J-STAGE: October 31, 2015
    DOIhttps://doi.org/10.5940/jcrsj.57.285
    JOURNAL FREE ACCESS
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    Phonon properties of lead titanate were investigated by measuring polarization-direction dependence of Raman intensities. Quantitative angle-resolved Raman spectroscopy is advantageous for detecting anisotropic nature of the sample material since that reflects the symmetry of vibrational modes. In this study, a broadband half-waveplate was utilized to establish high quantitativity, stability, and spatial reliability of the angle-resolved measurement.
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  • Structural Basis of the Assembly and Activation Mechanism of the Bacterial Flagellar Stator Complex
    Katsumi IMADA, Seiji KOJIMA
    2015 Volume 57 Issue 5 Pages 291-296
    Published: October 31, 2015
    Released on J-STAGE: October 31, 2015
    DOIhttps://doi.org/10.5940/jcrsj.57.291
    JOURNAL FREE ACCESS
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    Bacteria swim in aqueous environment by rotating the flagellum driven by a reversible motor embedded in the cell membrane. The torque of the motor is generated by the rotor-stator interaction coupled with the ion flow through the stator. A dozen of stators assemble around the rotor and are fixed to the peptidoglycan layer. The ion-conductivity of the stator is coupled to its assembly, and proper anchoring of the stator is required for torque generation. We determined the crystal structures of C-terminal fragments of the B-subunit of the stator including the region responsible for anchoring the stator, and performed the functional analyses using the mutants designed based on the structure. These studies revealed that the conformational change of the N-terminal region of the fragment is essential to form a functional stator around the rotor.
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  • Two Protonation States and Structural Features of a Bilin Reductase PcyA Revealed by Neutron Crystallography
    Masaki UNNO, Masakazu SUGISHIMA, Kei WADA, Yoshinori HAGIWARA, Katsuhi ...
    2015 Volume 57 Issue 5 Pages 297-303
    Published: October 31, 2015
    Released on J-STAGE: October 31, 2015
    DOIhttps://doi.org/10.5940/jcrsj.57.297
    JOURNAL FREE ACCESS
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    Bilin compounds are fundamentally important for oxygenic photosynthetic organisms, because they are utilized as pigments for photosynthesis (phycobilins) and photoreceptors (phytochromobilin). Phycocyanobilin (PCB), a phycobilin, comprises the chromophore of algal phytochromes and the core phycobiliprotein antennae of cyanobacteria and red algae. PCB is biosynthesized by a member of the ferredoxin-dependent bilin reductase family, phycocyanobilin:ferredoxin oxidoreductase (PcyA). In the present study, we determined the neutron crystal structure of PcyA in complex with its substrate biliverdin (BV). This neutron structure revealed the protonation state of BV and the surrounding residues. We found that two forms of BV, neutral BV and protonated BVH+, were coupled with the two conformation/protonation states of the essential residue Asp105. Further, His88 and His74 near BV were singly protonated and were connected with an intervening hydronium ion. Neutron analysis also revealed how X-ray irradiation of the PcyA-BV crystal altered the structure of the PcyA-BV complex.
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  • Structural Basis for the Regulation Mechanism of Synapse Formation
    Atsushi YAMAGATA, Shuya FUKAI
    2015 Volume 57 Issue 5 Pages 304-309
    Published: October 31, 2015
    Released on J-STAGE: October 31, 2015
    DOIhttps://doi.org/10.5940/jcrsj.57.304
    JOURNAL FREE ACCESS
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    Synapse formation is triggered through trans-synaptic interactions between selective pairs of pre- and postsynaptic adhesion molecules. Receptor tyrosine phosphatases (RPTP) can selectively interact with various postsynaptic adhesion molecules in a splicing-dependent manner. Here, we present our recent structural studies for the splicing-dependent regulation of the interactions between PTPδ and Interleukin-1 receptor accessory protein (IL-1RAcP)/ IL-1RAcP like 1 (IL1RAPL1).
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