Using a conformation-dependent stereochemical library improves crystallographic refinement of proteins

✍ Scribed by Tronrud, Dale E. ;Berkholz, Donald S. ;Karplus, P. Andrew

• Publisher: International Union of Crystallography
• Year: 2010
• Tongue: English
• Weight: 1021 KB
• Volume: 66
• Category: Article
• ISSN: 0907-4449
• DOI: 10.1107/s0907444910019207

✦ Synopsis

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 φ/ψ 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.