X-ray crystallographic refinement

Color-coded molecular surfaces can provide qualitative or quantitative displays of hydrophobic and hydrophilic regions, neutral and charged amino acid side chains, electrostatic potential, and conformational mobility of side chains (based on the temperature factors from X-ray crystallographic refinement or moelcular dynamics simulation). Color-coding by hydro-... 

There are two ways to model ADPs by normal modes in the literature. One is via direct calculation, whereby ADPs are directly derived from the atomic thermal fluctuations predicted by normal modes [12,42]. The other way, adopted in this study, is by a fitting procedure, in which ADPs are obtained by optimization against the experimental data, for example, diffraction data or experimental ADPs. The latter approach is chosen because it can produce more realistic ADPs according to several normal-mode-based x-ray crystallographic refinements [17,18,43,44] and other theoretical studies [45]. 

Fe(III)-CN bond ( 1.91 A) is longer (hence weaker) than the Fe(II)-CO bond ( 1.80 A). This result is at variance with the X-ray crystallographic findings of 2.2 and 2.4 A for the Fe-CN and Fe-CO bonds, respectively leading Yu to suggest that there may have been errors in the X-ray crystallographic refinement. 

These compounds have been extensively investigated because they are important nucleic acid constituents. Uracil has been shown conclusively to exist predominantly as pyrimidine-2,4-dione (99) both by a refined X-ray crystallographic technique in which the positions... 

X-ray crystallographic structures of the enzyme nitrogenase first became available in 1992 with refinements of the structures continuing to the present time. As of this... 

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. 

Fig. 35. The phosphonate analog of the carboxypeptidase A substrate Cbz-Ala-Ala-Phe inhibits the enzyme with a /fj of 3 pM (Hanson et al, 1989) and binds with unidentate phosphinyl-zinc coordination, as revealed in an X-ray crystallographic study (Kim and Lipscomb, 1990). Stippled density shows the refined positions of zinc and phosphorus. [Reprinted with permission from Kim, H., Lipscomb, W. N. (1990) Biochemistry 29, 5546-5555. Copyright 1990 American Chemical Society.]...

Salvinorin, isolated from Salvia divinorum has been shown by spectroscopic and X-ray-crystallographic methods to be a tran -neoclerodane diterpene of structure (1). Crystals of compound (1) are orthorhombic, space group P2iP2iP27 with a = 6.368 (2), h = 11.338(3), c = 30.7100 (6) A, and Z = 4. The structure was refined by least-squares to R 0.052 and R 0.056. 

The Structure of Atidine.—An X-ray crystallographic analysis of atidine [C22H33NO3 m.pt 182.3—183.5 °C] has been reported.21 This compound has been isolated from plants of Aconitum heterophyllum Wall. Its structure was solved by direct phasing methods and refined to a final R of 0.045. Since atidine... 

Another possibility cannot be ruled out in which the oxygen heterocyclic skeleton of daphnimacropine is identical with that of daphniphylline (1). Quite recently, further refinement of the X-ray crystallographic analysis5 of this methiodide has revealed it to have another... 

Determined by X-ray crystallographic analysis. b Solved by the direct-space approach using the Monte Carlo algorithm with the subsequent Rietveld refinement. 

The metastable y-form crystal structure prior to the slow phase transitions was determined by the X-ray crystallographic analysis, but the crystal structures of three other new polymorphs ( -, r)- and e-forms) were undetermined by the same X-ray analysis, because these polymorphs were obtained as powder samples. Since the nearly racemic e-form crystals could be obtained as the monophasic powder sample by just leaving the crystallization mixture untouched, its crystal structure was solved from its X-ray diffraction (XRD) data by the direct-space approach using the Monte Carlo algorithm with the subsequent Rietveld refinement.26,27 Consequently, the Rwp value has been satisfactorily converged to 9.1%. 

Structure and Absolute Configuration of Condelphine Hydroiodide.—Condel-phine, C25H39NO6, m.pt. 158—159 °C, has been isolated from Delphinium denu-datum and from D. confusum. This alkaloid was correlated with isotalatizidine (31) and talatizidine (32). On treatment with methyl iodide in a sealed tube at 80 °C, the hydroiodide derivative, rather than the methiodide, was obtained. X-Ray crystallographic structural investigations of this hydroiodide have shown the structure of condelphine to be (33), refined to R — 0.100, based on 3828 observed reflections.26... 

A set of atomic coordinates is obtained from X-ray crystallographic or NMR structure data, or by model building. The structure is first refined to relieve local stresses due to overlaps ofnon-bonded atoms, bond-length and angles distortions, etc. 

Finally, NMR-based structures will, in the foreseeable future, suffer from a poor ratio of data to degrees of freedom, when compared with X-ray crystallographic structures. This suggests that modeling based on NMR data will continue to rely on the quality of the force field used in refinements. Consequently, improvements in force fields will contribute to the quality of NMR structures as will the standard inclusion of solvents in refinement calculations. 

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