Refinement Crystal structure analysis

Wang, D., Bode, W., Huber, R. Bovine chymotrypsinogen A. X-ray crystal structure analysis and refinement of a new crystal form at 1.8 A resolution. /. Mol. Biol. 

A second example relates to the complex bis(l,5-diazacyclooctane)nickel(II) (Fig. 6.6). A crystal structure analysis of this complex revealed apparently planar NCCCN moieties with unusual bond lengths and angles 231. A molecular mechanics analysis of the same complex showed that these moieties are puckered and concluded that the crystal structure result was a consequence of conformational disorder, the refined geometry corresponding to an average of two puckered conformations (see Fig. 6.6)T24]. 

Preliminary three-dimensional atomic coordinates of atoms in crystal structures are usually derived from electron-density maps by fitting atoms to individual peaks in the map. The chemically reasonable arrangement of atoms so obtained is, however, not very precise. The observed structure amplitudes and their relative phase angles, needed to calculate the electron-density map, each contain errors and these may cause a misinterpretation of the computed electron-density map. Even with the best electron-density maps, the precisions of the atomic coordinates of a preliminary structure are likely to be no better than several hundredths of an A. In order to understand the chemistry one needs to know the atomic positions more precisely so that better values of bond lengths and bond angles will be available. The process of obtaining atomic parameters that are more precise than those obtained from an initial model, referred to as refinement of the crystal structure, is an essential part of any crystal structure analysis. 

The reader should be aware that there are cautions and limitations to be applied to the structural data derived by a crystal structure analysis. Interpretation of results must be made with an awareness of the precision of the coordinates being used, as discussed in Chapter 10. A description of terms used in statistical analyses of data and the resulting refined parameters is provided by Reference 17 which is recommended to the reader. 

The location of the hydrogen atom by the conventional methods of crystal structure analysis presents considerable difficulty, owing to its very small scattering power for X-rays. Although in a limited number of cases refined techniques have enabled hydrogen atoms to be directly located by X-ray diffraction, and although in a few other instances their... 

Figure 3. Flowchart of operations involved in evaluation of x-ray fiber diagram for polysaccharide crystal structure analysis left, experimental procedure and evaluation of fiber diagram right, computational refinement...

During the last few years the precision which is attainable in practical crystal-structure analysis has been greatly increased through the use of high-speed calculating equipment, especially of the punched-card type. With crystals of the complexity of an amino-acid or simple peptide, we formerly had to rely on the intensities of perhaps one or two hundred prism zone reflexions for establishing the positions of the atoms. Atomic co-ordinates were refined by the computation from these intensities of two-dimensional projections of electron density parallel... 

Brejc K, Ficner R, Huber R, and Steinbacher S. Isolation, crystallization, crystal structure analysis and refinement of allophycocyanin from the cyanobacterium Spirulina platenis at 2.3 A resolution. J Mol Biol. 1995 249 424-440. 

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... 

Bro] The alloy Cro.9Fei 1B0.9 (after wet ehemieal analysis) melted in zireonia emeible was examined using single erystal XRD. The crystal structure was refined it to be of the Mu4B type. 

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