title: X-ray refinement significantly underestimates the level of microscopic heterogeneity in biomolecular crystals.
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.
authors: Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria.
authors: Antonija
authors: A
authors: Kuzmanic
authors: Biophysical Structural Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands.
authors: Navraj S
authors: NS
authors: Pannu
authors: Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria.
authors: Bojan
authors: B
authors: Zagrovic
mesh_terms: D003460:Crystallization; D008840:Microfilament Proteins / Q000737:chemistry*; D056004:Molecular Dynamics Simulation
chemical_list: D008840:Microfilament Proteins; C026615:villin