Diffraction theory is presented for students who want to learn“black box”of the protein crystallography. The description that“the crystal works as a three dimensional diffraction lattice”is fully explained based on the wave nature of X-ray and the periodic nature of crystal. The reciprocal lattice is introduced as a means for calculating the lattice plane spacings. Using the reciprocal lattice, the diffraction condition is derived again with the concept of reflection sphere. The structure factor and the Fourier method are also introduced in the context of obtaining the electron density of the crystal.
The ultimate goal of diffraction experiments is to collect complete datasets as rapid as possible with good statistics. It is of atmost important that we should make the priority and objective of experiments clear to complete neccessary data acquisition in a fixed, short beamtime. Needless to say, we should select best beamlines for our objective in order to minimise time loss and to maximise the efficiency of the beamlines. Strategies of data acquisition on beamline X06SA at the Swiss Light Source is disscussed.
In the 1970's, the X-ray crystallographers have expected to use synchrotron radiation for further developing their researches. We have cooperated to construct the synchrotron radiation facilities, Photon Factory and SPring-8 from the user side. In this report I look back my activities in the user communities to realize the synchrotron radiation sources. Next, I describe some scientific achievements made using synchrotron radiation. They include the studies of X-ray dynamical diffraction, X-ray optics, X-ray surface diffraction, X-ray nuclear resonant scattering, and X-ray quantum optics.
At the SPring-8, we have developed and improved protein crystallography beamlines to achieve the data collection for High-Throughput Protein Crystallography. RIKEN Structural Biology Beamline I (BL45XU) is the first brunched Undulator beamline. The PX-station of BL45XU introduced the Trichromatic concept that optimizes for the multi-wavelength anomalous diffraction (MAD) method with three-colored and coaxial synchrotron X-ray beams. The concept enables rapid and flexible switching of three defined wavelengths and can be collected MAD data taking into account syatematic errors such as radiation damage. RIKEN Structural Genomics Beamlines (BL26B1 and BL26B2) have implemented the automatic operation for rapid data collection of a vast amount of protein crystals to contribute to the structural genomics research. The automation has been achieved by developing the centralized control software BSS. The nonstop data collections for multiple samples have been achieved by developing the new-concept sample changer SPACE. The automatic operation has been satisfactorily performed, for more than two years since 2003.
GGAs (Golgi-localizing, γ-adaptin ear homology domain, ARF-binding proteins) are a family of monomeric clathrin adaptor proteins that are conserved from yeasts to humans. The GGA molecule is composed of four functional regions : a VHS domain that interacts with TGN sorting receptors, such as mannose 6-phosphate receptors (MPR) ; a GAT domain that binds to the GTP-bound form of ARF; a hinge region that interacts with clathrin; a GAE domain interacts with accessory proteins. We have determined the crystal structures of VHS, GAT and AP-1 γ-ear domain that is the homolog of GAE domain. And we have also revealed the crystal structure of glucuronyltransferase, GlcAT-P which is critical enzyme in the biosynthesis of the carbohydrate epitope HNK-1.
The structural studies of powder diffraction using synchrotron radiation X-ray data have been described with some examples. The C2entrapping structure of yttrium di-metallofullerene has been determined by Maximum Entropy method (MEM) combined with Rietveld refinement. The MEM analysis of Zn4Sb3, which is one of the most efficient thermoelectric materials, has been presented by both powder and single crystal method. The structure determination of a single-component palladium complex with extended TTF-type dithiolate ligands has also been described.
The crystal structure of γ-P4, one of three modifications hitherto reported on white phosphorus was determined from X-ray powder diffraction data collected atT=123 K on a Guinier-Simon camera equipped with a cold gas blower and an image plate detector. The crystal structure of γ-P4was solved by the method of simulated annealing, and the subsequent Rietveld refinement in the range 12°<2θ<92°employing rigid-body constraints on the P4molecule converged atRp=3.8%, wRp=5.0%, andRF2=14.0%. The asymmetric unit of γ-P4contains three P atoms; two P atoms in a molecule are related by a mirror plane which bisects the molecule. The centers of gravity of these P4molecules show a distorted body-centered cubic (bcc) arrangement. The four apices of the P4tetrahedron point to the largest possible voids formed by neighbor molecules. The difference to the crystal structure of SiF4and GeF4with an exact bcc arrangement of tetrahedral molecules is discussed as well as, in terms of layer stackings, the similarity of the structures of γ- and β-P4.
The structures of many typical endohedral metallofullerenes have been reported by the powder X-ray analysis. For example, the report of the trimetallofullerene Sc3C82has shown that the endohedral structure is Sc3@C82, this being widely accepted. However, the recent13C NMR spectroscopy and X-ray single crystal analysis have revealed that the structure of Sc3C82is not Sc3@C82but Sc3C2@C80. This may suggest that the endohedral structures reported from the powder X-ray study are not always reliable even in a qualitative sense.