Structures from x-ray

Petsko G A and Ringe D 1984 Fluctuations in protein structure from x-ray diffraction A. Rev. Biophys. Bioengng. 13 331-71... 

A further milestone was achieved in 1977 by Richardson ct ah They could for the first time visualize a complete protein structure from X-ray ciystallography data 19h. A large numlier of structures were generated in the following years. 

Petsko, G. A., and Ringe, D., 1984. Fluctuations in protein structure from X-ray diffraction. Annual Review of Biophysics and Bioengineering 13 331 —371. 

X-rays. This was followed by the mathematical solution of crystal structure from X-ray diffraction data in 1913 by Bragg. Since that, many applications of X-ray were foimd including structure determination of fine-grained materials, like soils and days, which had been previously thought to be amorphous. Since then, crystals structures of the day minerals were well studied (Ray and Okamoto, 2003). 

The structure of the adsorbed ion coordination shell is determined by the competition between the water-ion and the metal-ion interactions, and by the constraints imposed on the water by the metal surface. This structure can be characterized by water-ion radial distribution functions and water-ion orientational probability distribution functions. Much is known about this structure from X-ray and neutron scattering measurements performed in bulk solutions, and these are generally in agreement with computer simulations. The goal of molecular dynamics simulations of ions at the metal/water interface has been to examine to what degree the structure of the ion solvation shell is modified at the interface. 

Polymerization of fullerite was first obtained at ambient pressure by means of sample irradiation [456]. Visible or UV light leads molecules to link together in a covalently bonded fee structure. From x-ray diffraction data a 2 + 2 cycloaddition mechanism was proposed in which the van der Waals interactions are replaced by single covalent bonds between adjacent Ceo molecules [456]. More recent results indicate that linear chains with two square rings per molecule or branched chains with three square rings per molecule are obtained... 

A complete structure determination contains the two distinct steps solving and refining the structure. The refinement can only be started after the structure has been solved. By solving a structure we mean that most of the most strongly scattering atoms are found to within an accuracy of 0.2 to 0.3 A. All methods for solving crystal structures from X-ray diffraction data in most cases give just a fraction of the complete structure. Patterson... 

Figure 1. Site energies (kcal/mole) of (GlcNAc)g bound to lysozyme. The total potential energy per site for residues A through F of (GlcNAc)g was calculated for the initial structure from X-ray and model building, E ) (A) for the average...

Main, P, Fiske, S. J., Hull, S. E., Lessinger, L., Germain, G., Declercq, J. P. and Woohson, M.M. (1980). MULTAN80 a System of Computer Programs for the Automatic Solution of Crystal Structures from X-ray Diffraction Data. Universities of York and Louvain. 

Fig. 15. Different perspectives of the methyl 2-deoxy-a-D-g/nco-septanoside (210) structure from X-ray data.

More than 200 structures from X-ray diffraction studies of acyclic organic peroxides have been disclosed in the literature since 1983. Structural information prior to 1983 was reviewed in an earlier book chapter and therefore has been omitted from this synopsis. Emphasis has been laid on a documentation of the most important structural information. The survey, however, remained incomplete since a considerable number of structures had been disclosed in the literature and/or the CSD database without providing the associated atomic coordinates. Further, structures with unusually short or long 0—0 connectivities have been omitted from the statistics for the reasons outlined in Section II. 

Certain mathematical techniques can determine molecular structure from X-ray diffraction images, such as this X-ray diffraction image of a protein. [Alfred Pasleka/Photo Researchers, Inc.]... 

Random structure methods have proved useful in solving structures from X-ray powder diffraction patterns. The unit cell can usually be found from these patterns, but the normal single-crystal techniques for solving the structure cannot be used. A variation on this technique, the reverse Monte Carlo method, includes in the cost function the difference between the observed powder diffraction pattern and the powder pattern calculated from the model (McGreevy 1997). It is, however, always necessary to include some chemical information if the correct structure is to be found. Various constraints can be added to the cost function, such as target coordination numbers or the deviation between the bond valence sum and atomic valence (Adams and Swenson 2000b Swenson and Adams 2001). 

Clear discussion of the regulatory changes in the structure of glycogen phosphorylase, based on the structures (from x-ray diffraction studies) of the active and less active forms of the enzyme. 

The determination of a molecular structure from X-ray diffraction data is of critical importance to modem chemical and biological sciences. For small molecules, the structure is normally determined by direct methods. The X-ray diffraction pattern resulting from the interaction of X-rays with the electron clouds of different elements gives a pattern from which the elements present and their connectivity may be deduced. The expected diffraction pattern calculated for an apparent structure is then compared with the observed data to refine the result. Refinement factors (usually expressed as Rw) of 1-3% are common in modem small molecule structure determinations. 

Commodari F, Khiat A, Ibrahimi S, Brizius AR, Kalkstein N. 2005. Comparison of the phytoestrogen, trans-resveratrol (3,4, 5 trihydroxystilbene) structures from X-Ray diffraction and solution NMR. Magn Reson Chem 43 567-572. 

Glick, M. and Goldblum, A. (2000) A novel energy-based stochastic method for positioning polar protons in protein structures from X-rays. Proteins Struct. Func. Gen. 38, 273-287. 

Yb-Cd-Sb. Salamakha and Mudryi (2001b) observed the YbCd2Sb2 compound and refined its crystal structure from X-ray powder diffraction data, CeAl2Si2 type structure, a = 0.46494, c = 0.75673. For the synthesis, see YbZn2Sb2. 

Cp HHKCioHilZrCp, CjhZtCU/K/C ioHb/ Dark-green solid. 19.3 (Zr-H) No Zr-H band Structure from X-ray 103... 

This material reacts with PMe3, forming an adduct (XLII) whose structure (from X-ray data) is shown below. 

The growth in available CYP protein structures from X-ray crystallography, presented in Figure 3, has inspired several investigators to detailed... 

As may clearly be seen from the examples described above, structure analysis cannot be an autonomous technique in solving structure from X-ray diffraction data when the structure is partially disordered. There is some more information... 

Stewart RF (1972) Valence structure from X-ray diffraction data physical properties. J. Chem. 

Valuable spectroscopic studies on the dithiolene chelated to Mo in various enzymes have been enhanced by the knowledge of the structure from X-ray diffraction. Plagued by interference of prosthetic groups—heme, flavin, iron-sulfur clusters—the majority of information has been gleaned from the DMSO reductase system. The spectroscopic tools of X-ray absorption spectroscopy (XAS), electronic ultraviolet/visible (UV/vis) spectroscopy, resonance Raman (RR), MCD, and various electron paramagnetic resonance techniques [EPR, electron spin echo envelope modulation (ESEEM), and electron nuclear double resonance (ENDOR)] have been particularly effective probes of the metal site. Of these, only MCD and RR have detected features attributable to the dithiolene unit. Selected results from a variety of studies are presented below, chosen because their focus is the Mo-dithiolene unit and organized according to method rather than to enzyme or type of active site. 

---