Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 106, Issue 43, Pages 18195-18200Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.0909287106
Keywords
multistart refinement; protein synthesis; ribosome dynamics; rRNA
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Funding
- National Institutes of Health and the National Science Foundation
- Danish Research Council
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A macromolecular X-ray crystal structure is usually represented as a single static model with a single set of temperature factors representing a simple approximation of motion and disorder of the structure. Multiconformer representations of small proteins have been shown to better describe anisotropic motion and disorder and improve the quality of their electron density maps. Here, we apply multistart simulated annealing crystallographic refinement to a 70S ribosome-RF1 translation termination complex that was recently solved at 3.2 angstrom resolution. The analysis improves the interpretability of the electron density map of this 2.5-MDa ribonucleoprotein complex and provides insights into its structural dynamics. We also used multistart refinement and conventional Fourier difference maps to address a recent study in which cross-crystal averaging between two crystal forms of the 70S ribosome was used to evaluate reported differences between two ribosome crystal structures solved at 2.8 and 3.7 angstrom resolution. Our analysis suggests that results obtained from cross-crystal averaging are inherently biased toward the higher-resolution dataset.
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