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H-atom Positions (h-atom + position)
Selected AbstractsIn-house characterization of protein powderJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 4 2010Christian Grundahl Hartmann X-ray powder diffraction patterns of lysozyme and insulin were recorded on a standard in-house powder diffractometer. The experimental powder diffraction patterns were compared with patterns calculated from Protein Data Bank coordinate data. Good agreement was obtained by including straightforward corrections for background, unit-cell parameters, disordered bulk solvent and geometric factors. In particular the solvent correction was found crucial for a good agreement. A revised Lorentz factor was derived, which gave a minor, but significant, improvement to the fit in the low-angle region. An attempt to include calculated H-atom positions did not improve the overall fit and was abandoned. The method devised was shown to be a quick and convenient tool for distinguishing precipitates and polymorphs of proteins. [source] Neutron protein crystallography: beyond the folding structure of biological macromoleculesACTA CRYSTALLOGRAPHICA SECTION A, Issue 1 2008Nobuo Niimura Neutron diffraction provides an experimental method of directly locating H atoms in proteins, a technique complementary to ultra-high-resolution X-ray diffraction. Three different types of neutron diffractometers for biological macromolecules have been constructed in Japan, France and the USA, and they have been used to determine the crystal structures of proteins up to resolution limits of 1.5,2.5,Å. Results relating to H-atom positions and hydration patterns in proteins have been obtained from these studies. Examples include the geometrical details of hydrogen bonds, the role of H atoms in enzymatic activity, CH3 configuration, H/D exchange in proteins and oligonucleotides, and the dynamical behavior of hydration structures, all of which have been extracted from these structural results and reviewed. Other techniques, such as the growth of large single crystals and a database of hydrogen and hydration in proteins, are described. [source] Structures of furanosides: geometrical analysis of low-temperature X-ray and neutron crystal structures of five crystalline methyl pentofuranosidesACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2001Artem Evdokimov Crystal structures of all five crystalline methyl d -pentofuranosides, methyl ,- d -arabinofuranoside (1), methyl ,- d -arabinofuranoside (2), methyl ,- d -lyxofuranoside (3), methyl ,- d -ribofuranoside (4) and methyl ,- d -xylofuranoside (5) have been determined by means of cryogenic X-ray and neutron crystallography. The neutron diffraction experiments provide accurate, unbiased H-atom positions which are especially important because of the critical role of hydrogen bonding in these systems. This paper summarizes the geometrical and conformational parameters of the structures of all five crystalline methyl pentofuranosides, several of them reported here for the first time. The methyl pentofuranoside structures are compared with the structures of the five crystalline methyl hexopyranosides for which accurate X-ray and neutron structures have been determined. Unlike the methyl hexopyranosides, which crystallize exclusively in the C1 chair conformation, the five crystalline methyl pentofuranosides represent a very wide range of ring conformations. [source] Redetermination of hydronium perchlorate at 193 and 293,KACTA CRYSTALLOGRAPHICA SECTION C, Issue 9 2003Azhar A. Rahman A sample of hydronium perchlorate, H3O+·ClO4,, crystallized from ethanol at ambient temperature, was found to be orthorhombic (space group Pnma) at both 193 and 293,K, with no phase transition observed in this temperature range. This contrasts with the earlier observation [Nordman (1962). Acta Cryst. 15, 18,23] of a monoclinic phase (space group P21/n) at 193,K for crystals grown at that temperature from perchloric acid. The hydronium and perchlorate ions lie across a mirror plane but it is not possible to define at either temperature a simple description of the H-atom positions due to the three-dimensional tumbling of the hydronium cation. [source] Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallographyACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2010Anna S. Gardberg The locations of H atoms in biological structures can be difficult to determine using X-ray diffraction methods. Neutron diffraction offers a relatively greater scattering magnitude from H and D atoms. Here, 1.65,Å resolution neutron diffraction studies of fully perdeuterated and selectively CH3 -protonated perdeuterated crystals of Pyrococcus furiosus rubredoxin (D-rubredoxin and HD-rubredoxin, respectively) at room temperature (RT) are described, as well as 1.1,Å resolution X-ray diffraction studies of the same protein at both RT and 100,K. The two techniques are quantitatively compared in terms of their power to directly provide atomic positions for D atoms and analyze the role played by atomic thermal motion by computing the , level at the D-atom coordinate in simulated-annealing composite D-OMIT maps. It is shown that 1.65,Å resolution RT neutron data for perdeuterated rubredoxin are ,8 times more likely overall to provide high-confidence positions for D atoms than 1.1,Å resolution X-ray data at 100,K or RT. At or above the 1.0, level, the joint X-ray/neutron (XN) structures define 342/378 (90%) and 291/365 (80%) of the D-atom positions for D-rubredoxin and HD-rubredoxin, respectively. The X-ray-only 1.1,Å resolution 100,K structures determine only 19/388 (5%) and 8/388 (2%) of the D-atom positions above the 1.0, level for D-rubredoxin and HD-rubredoxin, respectively. Furthermore, the improved model obtained from joint XN refinement yielded improved electron-density maps, permitting the location of more D atoms than electron-density maps from models refined against X-ray data only. [source] | ||||||||||