Geodesic
Unrestrained reciprocal space refinement of macromolecular structures as a tool to indicate alternative conformations
Matematičeskaâ biologiâ i bioinformatika, Tome 3 (2008) no. 2, pp. 50-59 
O. V. Sobolev; V. Yu. Lunin. Unrestrained reciprocal space refinement of macromolecular structures as a tool to indicate alternative conformations. Matematičeskaâ biologiâ i bioinformatika, Tome 3 (2008) no. 2, pp. 50-59. http://geodesic.mathdoc.fr/item/MBB_2008_3_2_a2/
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     title = {Unrestrained reciprocal space refinement of macromolecular structures as a~tool to indicate alternative conformations},
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     url = {http://geodesic.mathdoc.fr/item/MBB_2008_3_2_a2/}
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Voir la notice de l'article provenant de la source Math-Net.Ru

The detection of side chains in protein molecules that are present in crystal in alternative conformations is a laborious part of macromolecule structure determination by X-ray analysis. In our work we show, that significant changes of atom coordinates during X-ray refinement without stereochemical restraints may indicate the presence of alternative conformations.

[1] Engh R., Huber R., “Accurate bond and angle parameters for X-ray protein-structure refinement”, Acta Crystallogr D Biol Crystallogr., 47 (1991), 392–400

[2] Jaskolski M., Gilski M., Dauter Z., Wlodawer A., “Stereochemical restraints revisited: how accurate are refinement targets and how much should protein structures be allowed to deviate from them?”, Acta Cryst., 63 (2007), 611–620

[3] Sheldrick G. M., “Phase Annealing in SHELX-90: Direct Methods for Larger Structures”, Acta Cryst. A, 46 (1990), 467–473 | DOI

[4] Morris R. J., Bricogne G., “Sheldrick's 1.2 $\AA$ rule and beyond”, Acta Cryst. D, 59 (2003), 615–617 | DOI

[5] Bernstein F. C., Koetzle T. F., Williams G. J. B., Meyer E. F. Jr, Brice M. D., Rogers J. R., Kennard O., Shimanouchi T., Tasumi M., “The Protein Data Bank: a computer based archival file for macromolecular structures”, J. Mol Biol., 112 (1977), 535–547 | DOI

[6] Berman H. M., Westbrook J., Feng Z., Gilliland G., Bhat T. N., Weissig H., Shindyalov I. N., Bourne P. E., “The Protein Data Bank”, Nucleic Acids Res., 28 (2000), 235–242 | DOI

[7] Antson A. A., Smith D. J., Roper D. I., Lewis S., Caves L. S., Verma C. S., Buckley S. L., Lillford P. J., Hubbard R. E., “Understanding the mechanism of ice binding by type III Antifreeze Proteins”, J. Mol. Biol., 305 (2001) | DOI

[8] Kang B. S., Devedjiev Y., Derewenda U., Derewenda Z. S., “The Pdz2 domain of syntenin at ultra-high resolution: bridging the gap between small molecule and macromolecular crystal chemistry”, J. Mol. Biol., 338 (2004) | DOI

[9] Afonine P. V., Grosse-Kunstleve R. W., Adams P. S., “The Phenix refinement framework”, CCP4 Newsletters, 42 (2005), contribution 8