Macromolecular refinement of X-ray and cryoelectron microscopy structures with Phenix/OPLS3e for improved structure and ligand quality.
Structure
; 29(8): 913-921.e4, 2021 08 05.
Article
en En
| MEDLINE
| ID: mdl-33823127
ABSTRACT
With the advent of the resolution revolution in cryoelectron microscopy (cryo-EM), low-resolution refinement is common, and likewise increases the need for a reliable force field. Here, we report on the incorporation of the OPLS3e force field with the VSGB2.1 solvation model in the structure determination package Phenix. Our results show significantly improved structure quality and reduced ligand strain at lower resolution for X-ray refinement. For refinement of cryo-EM-based structures, we find comparable quality structures, goodness-of-fit, and reduced ligand strain. We also show how structure quality and ligand strain are related to the map-model cross-correlation as a function of data weight, and how that can detect overfitting. Signs of overfitting are found in over half of our cryo-EM dataset, which can be remedied by a re-refinement at a lower data weight. Finally, a start-to-end script for refining structures with Phenix/OPLS3e is available in the Schrödinger 2020-3 distribution.
Palabras clave
Texto completo:
1
Bases de datos:
MEDLINE
Asunto principal:
Proteínas
/
Sustancias Macromoleculares
Idioma:
En
Revista:
Structure
Asunto de la revista:
BIOLOGIA MOLECULAR
/
BIOQUIMICA
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BIOTECNOLOGIA
Año:
2021
Tipo del documento:
Article
País de afiliación:
Estados Unidos