In these years, 2D detectors (IP and CCD) are widely utilized in laboratory diffractmeters for analysing small molecular crystals. They are very convenient for rapid and high accuracy diffraction intensity measurement ; however, as they have opposite characteristics, the measurement strategy is also quite different. The author describes the general measurement procedures and tips in indexing, integration, and merging steps of IP and CCD diffractometers, mainly for novice or to-be users.
Our study of electron crystallography or convergent beam electron diffraction (CBED) and of electron spectroscopy or electron energy-loss spectroscopy (EELS), which were done from my student time until my retirement, is described together with other important results. All the crystal point groups can be determined unambiguously by CBED. Most crystal space groups are determined by using dynamical extinction effect and coherent CBED. The large angle technique enables us to determine the characteristic features of the lattice defects more reliably than the traditional electron microscope method. Using the energy filtering technique, the crystal structure refinement is successfully carried out by fitting the experimental CBED pattern with the theoretically calculated pattern. A case study of the determination of a charge density distribution is shown. A high energy resolution EELS instrument (< 0.1 eV) was developed for the study of electronic structures or the structure of the conduction band. A case study of a detailed band structure is shown with a theoretical calculation. A clean application to fullerenes is shown. A recent development of the wavelength dispersive spectroscopy attachment is mentioned.
Manipulation of molecular crystals formed from self-organization is one of important methods to develop the new molecular functional materials. We have been looking upon in particular mutual cohesive interactions of hydrogen bonding and metal coordination as one of useful tools to construct the preprogramming super-structures. In this study, four controlled super-structures of a one-dimensional linear chain, a zig-zag ribbon, right-handed and lefthanded helices, and a two-dimensional honeycomb sheet are newly created by using the neutral metal complexes with some 2, 2'-biimidazolate mono-anions.
A novel method for eliminating instrumental aberrations from powder X-ray diffraction data has been developed. The method is based on fast Fourier transformation (FFT) combined with abscissa-scale transformation appropriately modeled for each instrumental aberration. All the main aberrations of laboratory powder diffractometer with Bragg-Brentano geometry, (1) Kα2 subpeak, (2) axial-divergence aberration, (3) flat-specimen aberration, and (4) sample transparency effect, can be automatically removed from the whole powder diffraction data ranging wide diffraction angles in quite a simple procedure. Propagation of the statistical errors attached to the source data through the Fourier transformation is also discussed.
Multi-drug resistance of pathogenic bacteria often results from the over-expression of the multi-drug efflux system. AcrB is a major multi-drug efflux transporter protein in E.coli that exports wide variety of drugs, antibiotics and toxic compounds. We have solved the crystal structure of AcrB at 3.5 angstrom resolution. Three AcrB monomers are organized as a trimer. Each monomer is composed of 12 transmembrane α-helices and a 70 angstrom protruding hydrophilic region in periplasmic space. This is the first crystal structure of drug transporter, and also the first atomic-level structure of a secondary transporter which driven by proton motive force across the plasma membrane.
Copper-containing amine oxidase contains a covalently bound organic cofactor, 2, 4, 5-trihydroxyphenylalanine (topa) quinone, which is formed by post-translational modification of a specific tyrosine residue in the presence of copper ion and oxygen molecule. Apo-enzyme crystals were anaerobically soaked in the mother liquor that contains copper ion and were freezetrapped to determine the initial structure of the biogenesis. In order to see the structures in the following stages, we started the reaction by exposing the copper-bound crystals to the air, and freeze-trapped them immediately, and also trapped long after the exposure. The structures of three district intermediates have been determined. The molecular mechanism of the topa quinone biogenesis will be discussed on the basis of these X-ray snapshots.
Structural Genomics has launched over the world including National Project of Protein Structural and Functional Analysis in Japan in a post-genomic era. It remains many bottlenecks to determine the protein structures with SR protein crystallography based on full-genome sequence information in high throughput manner. We review the bottlenecks and pit falls in the high throughput technologies from expression plasmid to protein structure in account of our experience of RIKEN Highthroughput Factory at SPring-8.