ArticleNature communications2014
X-ray refinement significantly underestimates the level of microscopic heterogeneity in biomolecular crystals.
Article in Nature communications, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed.
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- Bayesian multi-state multi-condition modeling of a protein structure based on X-ray crystallography data.bioRxiv : the preprint server for biology · 2025Article
- Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction.bioRxiv : the preprint server for biology · 2025Article
- The stability and self-assembly of tri-calcium silicate and hydroxyapatite scaffolds in bone tissue engineering applications.Journal of biological engineering · 2025Article
- Ligand-based pharmacophore modeling and machine learning for the discovery of potent aurora A kinase inhibitory leads of novel chemotypes.Molecular diversity · 2024Article
- Assessment of Four Theoretical Approaches to Predict Protein Flexibility in the Crystal Phase and Solution.Journal of chemical theory and computation · 2024Article
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- Functional protein dynamics in a crystal.Nature communications · 2024Article
- Functional Protein Dynamics in a Crystal.bioRxiv : the preprint server for biology · 2024Article
- New Crystal Form of Human Neuropilin-1 b1 Fragment with Six Electrostatic Mutations Complexed with KDKPPR Peptide Ligand.Molecules (Basel, Switzerland) · 2023Article
- Binding site plasticity regulation of the FimH catch-bond mechanism.Biophysical journal · 2023Article
- Synergism between x-ray crystallography and NMR residual dipolar couplings in characterizing protein dynamics.Structural dynamics (Melville, N.Y.) · 2023Article
- Refinement of multiconformer ensemble models from multi-temperature X-ray diffraction data.Methods in enzymology · 2023Article
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- Ensemble-function relationships to dissect mechanisms of enzyme catalysis.Science advances · 2022Article
- Evaluating the impact of X-ray damage on conformational heterogeneity in room-temperature (277 K) and cryo-cooled protein crystals.Acta crystallographica. Section D, Structural biology · 2022Article
- Functional roles of enzyme dynamics in accelerating active site chemistry: Emerging techniques and changing concepts.Current opinion in structural biology · 2022Review
- Mapping Enzyme Landscapes by Time-Resolved Crystallography with Synchrotron and X-Ray Free Electron Laser Light.Annual review of biophysics · 2022Review
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3 authors.
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Abstract
Biomolecular X-ray structures typically provide a static, time- and ensemble-averaged view of molecular ensembles in crystals. In the absence of rigid-body motions and lattice defects, B-factors are thought to accurately reflect the structural heterogeneity of such ensembles. In order to study the effects of averaging on B-factors, we employ molecular dynamics simulations to controllably manipulate microscopic heterogeneity of a crystal containing 216 copies of villin headpiece. Using average structure factors derived from simulation, we analyse how well this heterogeneity is captured by high-resolution molecular-replacement-based model refinement. We find that both isotropic and anisotropic refined B-factors often significantly deviate from their actual values known from simulation: even at high 1.0 Å resolution and Rfree of 5.9%, B-factors of some well-resolved atoms underestimate their actual values even sixfold. Our results suggest that conformational averaging and inadequate treatment of correlated motion considerably influence estimation of microscopic heterogeneity via B-factors, and invite caution in their interpretation.
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