Refinement crystallographic

Page 1176 (Figure 28 11) is adapted from crystallographic coordinates deposited with the Protein Data Bank PDB ID 6TNA Sussman J L Holbrook S R Warrant R W Church G M Kim S H Crystal Structure of Yeast Phenylalanine tRNA I Crystallographic Refinement / Mol Biol 1978 126 607 (1978)... 

Schneider, G., Lindqvist, Y., Lundqvlst, T. Crystallographic refinement and structure of ribulose-1,5-bisphosphate carboxylase from Rhodospirillum rubrum at 1.7 A resolution. J. Mol. Biol. 

Fehlhammer, H., Bode, W., Huber, R. Crystal structure of bovine trypsinogen at 1.8 A resolution. 11. Crystallographic refinement, refined crystal structure and comparison with bovine trypsin. J. Mol. Biol. 

Deisenhofer, J. Crystallographic refinement and atomic models of a human Fc fragment and its complex with fragment B of protein A from Staphylococcus aureus at 2.9 and 2.8 A resolution. Biochemistry 20 2361-2369, 1981. 

Jones, T.A., Liljas, L. Structure of satellite tobacco necrosis virus after crystallographic refinement at 2.5 A resolution. /. Mol. Biol. 177 735-768, 1984. 

Recently Blake et al.153) made such studies in the case of human (HL) and tortoise egg-white (TEWL) lysozyme based on crystallographic refinements at 1,5 and 1,6 A resolution, respectively. By these investigations they attempted to obtain information on the perturbations of water structure in the hydration shell by neighboured protein molecules and by high salt concentrations as well as on the degree of order of the bound water. The authors came to the conclusion that the number of ordered water molecules are 128 in TEWL and 140 in HL, whereas the overall content is made up of 650 and 350 water molecules per lysozyme molecule. 

The atomic temperature factors obtained after crystallographic refinement are significantly higher for cys530 than for the other site cysteine residues. This is also true when the Ni ion is compared to the Fe center. This may reflect conformational disorder due to the fact that the crystals are made of a mixture of different Ni states (40% Ni-A, 10% Ni-B, and 50% of an EPR-silent species) (52). 

Crystallographic refinement is a procedure which iteratively improves the agreement between structure factors derived from X-ray intensities and those derived from a model structure. For macro molecular refinement, the limited diffraction data have to be complemented by additional information in order to improve the parameter-to-observation ratio. This additional information consists of restraints on bond lengths, bond angles, aromatic planes, chiralities, and temperature factors. 

Briinger A, Karpins M, Petsko GA. Crystallographic refinement by simulated annealing application to crambin. Acta Crystallogr, Sect A 1989 A45 50-61. 

Brunger AT (1988) Crystallographic refinement by simulated annealing. Application to a 2.8 A resolution structure of aspartate aminotransferase. J Mol Biol 203(3) 803-816... 

In the case of ITPP, Ferro and BrCickner (28) showed that unrestrained minimization of the total energy for a microcrystal corresponding to unstretched fibers yields a structure in very close agreement to the crystallographically refined one. This was in contrast to the earlier results with less accurate calculations. Furthermore, their calculations, which used slightly modified MM2 potentials and a modest restraint on the cartesian coordinates, provided a stereochemically acceptable model that reproduces the powder diffraction profile as accurately as the least-squares fitted model. 

Macromolecular crystallographic refinement is an example of a restrained optimization problem. Standard refinement programs adjust the atomic positions and, typically, also their atomic displacement parameters of a given model with the... 

Figure 11.3 The ratio of the number of reflections to the number of parameters in the XYZB crystallographic refinement of a protein model as a function of the resolution of the data. The data are assumed to be complete and the solvent content to be 50%.

Romo, T.D., Clarage, J.B., Sorensen, D.C., Phillips, G.N. Automatic identification of discrete substates in proteins-singular-value decomposition analysis of time-averaged crystallographic refinements. Proteins 1995, 22, 311-21. 

At present two three-dimensional structures are available, one determined by the 2D-NMR for solution protein (Cd,MT) and the other using the conventional crystallographic method . These are in conflict and major discrepancies exist between the two structures. In addition, in the recent crystallographic refinement where metal-sulphur clusters were also refined, metal-sulphur bond distances are obtained which are in serious error with respect to the EXAFS determined distances despite the claimed accuracy. For example, the Cd—S distances show considerable variation from 2.5 A the average terminal ligand distance is 3.2 A while the bridging... 

The initial model of ALBP was built by simply putting the amino acid sequence of ALBP into the molecular structure of myelin P2 protein. After a 20-step rigid-body refinement of the positions and orientations of the molecule, crystallographic refinement... 

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