Journal
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
Volume 66, Issue -, Pages 834-842Publisher
INT UNION CRYSTALLOGRAPHY
DOI: 10.1107/S0907444910019207
Keywords
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Funding
- National Institutes of Health [R01-GM083136]
- National Science Foundations [MCB-9982727]
- National Institute of Environmental Health Sciences [P30 ES00210]
- US Department of Energy, Basic Energy Sciences, Office of Science [DE-AC02-06CH11357]
- National Institutes of Health, National Center for Research Resources [RR007707]
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The major macromolecular crystallographic refinement packages restrain models to ideal geometry targets defined as single values that are independent of molecular conformation. However, ultrahigh-resolution X-ray models of proteins are not consistent with this concept of ideality and have been used to develop a library of ideal main-chain bond lengths and angles that are parameterized by the phi/psi angle of the residue [Berkholz et al. (2009), Structure, 17, 1316-1325]. Here, it is first shown that the new conformation-dependent library does not suffer from poor agreement with ultrahigh-resolution structures, whereas current libraries have this problem. Using the TNT refinement package, it is then shown that protein structure refinement using this conformation-dependent library results in models that have much better agreement with library values of bond angles with little change in the R values. These tests support the value of revising refinement software to account for this new paradigm.
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