title: Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution.
abstract: Traditional methods for macromolecular refinement often have limited success at low resolution (3.0-3.5 Å 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 ϕ,ψ 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).
authors.affiliation: Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. jjheadd@lbl.gov
authors.forename: Jeffrey J
authors.initials: JJ
authors.lastname: Headd
authors.forename: Nathaniel
authors.initials: N
authors.lastname: Echols
authors.forename: Pavel V
authors.initials: PV
authors.lastname: Afonine
authors.forename: Ralf W
authors.initials: RW
authors.lastname: Grosse-Kunstleve
authors.forename: Vincent B
authors.initials: VB
authors.lastname: Chen
authors.forename: Nigel W
authors.initials: NW
authors.lastname: Moriarty
authors.forename: David C
authors.initials: DC
authors.lastname: Richardson
authors.forename: Jane S
authors.initials: JS
authors.lastname: Richardson
authors.forename: Paul D
authors.initials: PD
authors.lastname: Adams
mesh_terms: D020029:Base Pairing; D018360:Crystallography, X-Ray / Q000379:methods*; D004247:DNA / Q000032:analysis / Q000737:chemistry; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000032:analysis / Q000737:chemistry; D012984:Software
chemical_list: D011506:Proteins; D004247:DNA