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Model validation: local diagnosis, correction and when to quit.

Jane S Richardson1, Christopher J Williams1, Bradley J Hintze1

  • 1Department of Biochemistry, Duke University, Durham, NC 27710, USA.

Acta Crystallographica. Section D, Structural Biology
|March 14, 2018
PubMed
Summary
This summary is machine-generated.

Model validation should actively guide corrections throughout structure solution, prioritizing local geometry and conformations over global measures for improved results. Crystallographers must still correct outliers, focusing on density and functional reasons for valid findings.

Keywords:
MolProbityall-atom contactslikelihoodoutlier correctionstructure validation

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Area of Science:

  • Structural Biology
  • X-ray Crystallography
  • Biochemical Modeling

Background:

  • Traditional model validation acts as a final check.
  • Refinement benefits from continuous validation guidance.

Purpose of the Study:

  • Shift validation emphasis from global to local measures.
  • Improve structure solution accuracy and efficiency.

Main Methods:

  • Focus on local geometry, conformations, and sterics.
  • Utilize explicit hydrogen atoms for steric criteria.
  • Employ 'Backrub' motions for side chains and 'P-perp' diagnostics for ribose puckers.
  • Apply CaBLAM for protein secondary structure and ERRASER for RNA backbone at low resolution.

Main Results:

  • Local minimum misfits generate multiple outliers.
  • Prioritizing correct local minima improves refinement.
  • Alternate conformations and non-ideal features (e.g., water as ions) require careful consideration.
  • High-resolution modeling should include alternate conformations; low-resolution requires specific diagnostic tools.

Conclusions:

  • Active validation throughout structure solution enhances refinement.
  • Crystallographers remain essential for outlier correction within density context.
  • A small number of outliers is expected, with functional reasons sought for valid ones.