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Related Experiment Videos

Reliability of atomic displacement parameters in protein crystal structures.

O Carugo1, P Argos

  • 1European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany and Department of General Chemistry of the University, Via Taramelli 12, 27100 Pavia, Italy. carugo@embl-heidelberg.de

Acta Crystallographica. Section D, Biological Crystallography
|March 25, 1999
PubMed
Summary

Standard errors in atomic displacement parameters (ADPs) of protein structures increase with lower resolution and are larger for exposed or helical atoms. These findings inform comparisons of protein structures and the impact of refinement restraints.

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Area of Science:

  • Structural Biology
  • Crystallography
  • Biophysics

Background:

  • Atomic displacement parameters (ADPs) quantify atomic motion in protein crystals.
  • Accurate estimation of ADP standard errors is crucial for reliable structural comparisons.
  • Crystallographic refinement involves restraints that can influence ADP values.

Purpose of the Study:

  • To estimate mean standard errors in atomic displacement parameters (ADPs) from protein crystal structure determinations.
  • To investigate factors influencing ADP standard errors, including resolution and atomic environment.
  • To assess the impact of crystallographic refinement restraints on ADP standard errors.

Main Methods:

  • Comparing ADPs of identical protein-chain pairs within the same or different crystals.

Related Experiment Videos

  • Analyzing ADP standard errors in relation to crystallographic resolution.
  • Differentiating ADP standard errors based on atom type (main-chain vs. side-chain) and solvent accessibility.
  • Evaluating differences in ADP standard errors for residues in helical versus other secondary structures.

    • Main Results:

    • ADP standard errors increase nearly linearly with decreasing resolution.
    • ADP standard errors are greater for side-chain and solvent-exposed atoms compared to main-chain and buried atoms.
    • Residues in helical secondary structures exhibit larger ADP standard errors than those in other conformations.
    • The study provides insights into the influence of crystallographic refinement restraints on ADP standard errors.

    Conclusions:

    • The resolution dependence of ADP standard errors is unexpectedly linear.
    • Atomic environment and secondary structure significantly impact ADP uncertainty.
    • Corrections for refinement restraint influences are recommended when comparing protein structures.