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Related Experiment Videos

Why protein R-factors are so large: a self-consistent analysis.

Dennis Vitkup1, Dagmar Ringe, Martin Karplus

  • 1Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454-9110, USA.

Proteins
|February 9, 2002
PubMed
Summary

Protein X-ray crystallography R-factors are often high due to modeling anisotropic motions with isotropic B-factors and coordinate errors. These factors significantly inflate R-factor values beyond experimental data limitations.

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Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • R-factor and R-free are key metrics for assessing protein model quality in X-ray crystallography.
  • Typical R-factors for well-refined structures range from 20-25%, contrasting with ~5% intrinsic experimental error.

Purpose of the Study:

  • To identify major contributors to high protein R-factor values using molecular dynamics simulations.
  • To perform a self-consistent analysis of factors influencing R-factor accuracy.

Main Methods:

  • Utilized molecular dynamics (MD) simulations for a self-consistent analysis.
  • Investigated the impact of isotropic B-factors and coordinate errors on R-factors.

Main Results:

  • Significant R-factor inflation can result from using isotropic B-factors for anisotropic motions.

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  • Coordinate errors also contribute substantially, with similar impact to B-factor inaccuracies for errors < 0.2 Å.
  • Isotropic B-factors alone can increase R-factors by ~10% even without coordinate errors.

    • Conclusions:

    • Anisotropic protein motions modeled with isotropic B-factors and coordinate errors are primary drivers of high R-factors.
    • Inaccurate energy functions and multistate protein dynamics are unlikely to be major contributors to elevated R-factors.