ArticleStructure (London, England : 1993)2021
Macromolecular refinement of X-ray and cryoelectron microscopy structures with Phenix/OPLS3e for improved structure and ligand quality.
Article in Structure (London, England : 1993), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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41 citing papers in PubMed.
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- Critical evaluation of three cryo-EM structures of particulate methane monooxygenase by quantum refinement.Acta crystallographica. Section D, Structural biology · 2025Article
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- NPF binding to Arp2 is allosterically linked to the release of ArpC5's N-terminal tail and conformational changes in Arp2/3 complex.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Structural basis of disease mutation and substrate recognition by the human SLC2A9 transporter.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Mechanism of actin filament severing and capping by gelsolin.Nature structural & molecular biology · 2025Article
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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.
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