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Related Experiment Videos

Checking nucleic acid crystal structures.

U Das1, S Chen, M Fuxreiter

  • 1Service de Conformation de Macromolécules Biologiques et Bioinformatique, Université Libre de Bruxelles, Avenue F. D. Roosevelt 50, CP160/16, B-1050 Bruxelles, Belgium.

Acta Crystallographica. Section D, Biological Crystallography
|May 26, 2001
PubMed
Summary
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This study evaluated 105 nucleic acid crystal structures using SFCHECK, finding most structures are uniformly good quality. However, some water molecule positions showed poor electron density, suggesting potential issues in the overall model.

Area of Science:

  • Crystallography
  • Structural Biology
  • Bioinformatics

Background:

  • Evaluating the quality of nucleic acid crystal structures is challenging due to molecular symmetry.
  • Structure-factor data and atomic coordinates require rigorous assessment for reliability.

Purpose of the Study:

  • To survey the quality of 105 nucleic acid crystal structures using the SFCHECK program.
  • To assess agreement between structure-factor data and atomic coordinates.
  • To identify potential issues in crystallographic models, particularly water molecule positions.

Main Methods:

  • Utilized the SFCHECK program to analyze structure-factor amplitudes and atomic coordinates.
  • Evaluated overall structure quality using parameters like R factor and correlation coefficient.

Related Experiment Videos

  • Assessed local quality using indicators such as atomic displacement, density correlation, B factor, and density index.

    • Main Results:

    • Most nucleic acid structures exhibit uniform quality, with global indicators varying linearly with resolution.
    • Atomic coordinates of nucleic acid bases are generally better defined than the backbone.
    • The density index revealed that a significant fraction of crystallographic water positions have poorly defined electron density.

    Conclusions:

    • Nucleic acid crystal structure quality is generally consistent, but local indicators highlight specific areas for improvement.
    • Poorly defined water molecules may indicate broader problems within the crystallographic model.
    • The density index is a valuable tool for identifying unreliable regions in structural models.