Journal
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
Volume 68, Issue -, Pages 381-390Publisher
INT UNION CRYSTALLOGRAPHY
DOI: 10.1107/S0907444911047834
Keywords
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Funding
- NIH [GM063210]
- ARRA supplement
- PHENIX Industrial Consortium
- US Department of Energy [DE-AC02-05CH11231]
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Traditional methods for macromolecular refinement often have limited success at low resolution (3.0-3.5 angstrom or worse), producing models that score poorly on crystallographic and geometric validation criteria. To improve low-resolution refinement, knowledge from macromolecular chemistry and homology was used to add three new coordinate-restraint functions to the refinement program phenix.refine. Firstly, a 'reference-model' method uses an identical or homologous higher resolution model to add restraints on torsion angles to the geometric target function. Secondly, automatic restraints for common secondary-structure elements in proteins and nucleic acids were implemented that can help to preserve the secondary-structure geometry, which is often distorted at low resolution. Lastly, we have implemented Ramachandran-based restraints on the backbone torsion angles. In this method, a phi,psi term is added to the geometric target function to minimize a modified Ramachandran landscape that smoothly combines favorable peaks identified from nonredundant high-quality data with unfavorable peaks calculated using a clash-based pseudo-energy function. All three methods show improved MolProbity validation statistics, typically complemented by a lowered R-free and a decreased gap between R-work and R-free.
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