Crystal structure analysis data collection

Crystallographic structure refinement is generally understood to be the last step in the determination of a crystal structure by diffraction methods. The usual procedure of a crystal structure analysis includes collection of X-ray or neutron diffraction intensities, data reduction yielding structure factor amplitudes, the solution of the crystallographic phase problem yielding approximate structural parameters and finally refinement of these parameters to obtain a best fit of the observed structure factor amplitudes with... 

X-ray single crystal analysis Data collection. Siemens SMART IK CCD. Diffractometer. Data collection by SMART (Siemens, 1995) cell refinement SMART data reduction SAINT (Siemens, 1995) program(s) used to solve structure SHELXS97 (Sheldrick, 1997) program(s) used to refine structure SHELXL97 (Sheldrick, 1997) molecular graphics XP in SHELXTL (Sheldrick,... 

Before the mechanism of the racemic-to-chiral transformation and inversion processes are examined, it may be better to explain the solid-state photoreaction with retention of the single crystal form, which is called a crystalline-state reaction. We found that the chiral 1-cyanoethyl group, bonded to the cobalt atom in 4 cobaloxime complex crystal, was racemized on exposure to x-rays or visible light [13]. Since the crystallinity was kept in the whole process of the racemization the intensity data were collected at any stage of the reaction, and the process of the structural change was observed by x-ray crystal structure analysis. The change of the unit cell dimensions with time, which was well explained by first-order kinetics, corresponded to the rate of racemization [14] (Scheme 1). ... 

Although crystal structure analysis was once a very time consuming and very expensive process, this has not been the case for a number of years. Structural results are usually available within two weeks of when a crystal is placed on the diffractometer instrument. This change has been due to a number of factors. Computer-controlled diffractometers have made data collection more accurate and much easier. The process of obtaining a trial structure has been much facilitated by the use of computerized direct methods and by computer graphics. 

A diffractometer is a compnter-controlled instrument nsed for carrying out the X-ray analysis of crystals. It rotates the crystal with respect to the X-ray beam and collects the data produced by the scattering of the X rays from the various planes of atoms in the crystal. The results are then analyzed by computer. The techniques for crystal structure analysis have reached a level of sophistication that allows the determination of very complex structures, such as those important in biological systems. Using X-ray diffraction, we can... 

The importance of water in the preceding structure and theoretical considerations of its role suggested growing crystals in a water-free environment. The resulting crystals of unhydrated 1 Im were, in general, hardly suitable for X-ray analysis. Nevertheless, out of interest, data collection from a rather small crystal was attempted. The subsequent analysis gave the structural model11 u as depicted in Fig. 45. 

X-ray structural analysis. Suitable crystals of compound 14 were obtained from toluene/ether solutions. X-ray data were collected on a STOE-IPDS diffractometer using graphite monochromated Mo-Ka radiation. The structure was solved by direct methods (SHELXS-86)16 and refined by full-matrix-least-squares techniques against F2 (SHELXL-93).17 Crystal dimensions 0.3 0.2 0.1 mm, yellow-orange prisms, 3612 reflections measured, 3612 were independent of symmetry and 1624 were observed (I > 2ct(7)), R1 = 0.048, wR2 (all data) = 0.151, 295 parameters. 

Once a suitable crystal is obtained and the X-ray diffraction data are collected, the calculation of the electron density map from the data has to overcome a hurdle inherent to X-ray analysis. The X-rays scattered by the electrons in the protein crystal are defined by their amplitudes and phases, but only the amplitude can be calculated from the intensity of the diffraction spot. Different methods have been developed in order to obtain the phase information. Two approaches, commonly applied in protein crystallography, should be mentioned here. In case the structure of a homologous protein or of a major component in a protein complex is already known, the phases can be obtained by molecular replacement. The other possibility requires further experimentation, since crystals and diffraction data of heavy atom derivatives of the native crystals are also needed. Heavy atoms may be introduced by covalent attachment to cystein residues of the protein prior to crystallization, by soaking of heavy metal salts into the crystal, or by incorporation of heavy atoms in amino acids (e.g., Se-methionine) prior to bacterial synthesis of the recombinant protein. Determination of the phases corresponding to the strongly scattering heavy atoms allows successive determination of all phases. This method is called isomorphous replacement. 

The precision structure analysis of crystals and quantitative reconstruction of ESP requires the maximum possible set of structure amplitudes, which would provide a precise scaling factor, information on the thermal atomic motion and the high resolution of the ESP with good statistical accuracy being at least 1-2%. Such an experimental data set can be collected by an electron diffractometer which was designed on the basis of EMR-102 [3] (Fig. 3). 

KcsA crystals suitable for X-ray crystallographic analysis using synchrotron radiation were obtained and the data collected and analyzed for multiple crystals and six different data sets as described in the 1998 Science publication (reference 15). The final KcsA pore structure, including amino acid residues 23 to 119 of the K+ channel, refined to 3.2 A. The X-ray data were deposited in the Protein Data Bank with the accession number 1BL8. 

Once Te-III was identified as incommensurate, subsequent analysis was conducted on the previously-collected powder-diffraction data using the formalism of 4D superspace [234], and the JANA2000 software for structure refinement [235]. The Rietveld refinement of the incommensurate Te-III diffraction profile is shown in Fig. 9, and the modulated structure is shown in Fig. 10. Tellurium was only the second element found to have a modulated crystal structure at high-pressure, the... 

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