DOI: 10.1107/s0907444911047834. Use of knowledge-based restraints in <i>phenix.refine</i> to improve macromolecular refinement at low resolution

Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution

10.1107/s0907444911047834

Crossref journal-article

International Union of Crystallography (IUCr)

Acta Crystallographica Section D Biological Crystallography (329)

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.

Bibliography

Headd, J. J., Echols, N., Afonine, P. V., Grosse-Kunstleve, R. W., Chen, V. B., Moriarty, N. W., Richardson, D. C., Richardson, J. S., & Adams, P. D. (2012). Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution. Acta Crystallographica Section D Biological Crystallography, 68(4), 381â390.

Authors 9

Jeffrey J. Headd (first)
Nathaniel Echols (additional)
Pavel V. Afonine (additional)
Ralf W. Grosse-Kunstleve (additional)
Vincent B. Chen (additional)
Nigel W. Moriarty (additional)
David C. Richardson (additional)
Jane S. Richardson (additional)
Paul D. Adams (additional)

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Dates

Type	When
Created	13 years, 5 months ago (March 15, 2012, 12:38 p.m.)
Deposited	7 months, 1 week ago (Jan. 13, 2025, 6:07 a.m.)
Indexed	20 hours, 19 minutes ago (Aug. 23, 2025, 1:07 a.m.)
Issued	13 years, 5 months ago (March 16, 2012)
Published	13 years, 5 months ago (March 16, 2012)
Published Online	13 years, 5 months ago (March 16, 2012)
Published Print	13 years, 4 months ago (April 1, 2012)

Funders 0

None

BibTeX

@article{Headd_2012, title={Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution}, volume={68}, ISSN={0907-4449}, url={http://dx.doi.org/10.1107/s0907444911047834}, DOI={10.1107/s0907444911047834}, number={4}, journal={Acta Crystallographica Section D Biological Crystallography}, publisher={International Union of Crystallography (IUCr)}, author={Headd, Jeffrey J. and Echols, Nathaniel and Afonine, Pavel V. and Grosse-Kunstleve, Ralf W. and Chen, Vincent B. and Moriarty, Nigel W. and Richardson, David C. and Richardson, Jane S. and Adams, Paul D.}, year={2012}, month=mar, pages={381–390} }

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