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Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard.

Thomas C Terwilliger1, Ralf W Grosse-Kunstleve, Pavel V Afonine

  • 1Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA. terwilliger@lanl.gov

Acta Crystallographica. Section D, Biological Crystallography
|December 21, 2007
PubMed
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The PHENIX AutoBuild wizard automates protein model building and refinement. This tool effectively completes models and refines structures, achieving good results across various resolutions.

Area of Science:

  • Structural biology
  • Computational biology
  • Biochemistry

Background:

  • Automated tools are crucial for accelerating the process of macromolecular structure determination.
  • Iterative model building, structure refinement, and density modification are key steps in solving protein structures.
  • Existing methods often require significant manual intervention, limiting throughput.

Purpose of the Study:

  • To introduce and evaluate the enhanced PHENIX AutoBuild wizard for automated macromolecular model building and refinement.
  • To showcase advancements in automated detection of non-crystallographic symmetry (NCS), model completion, and solvent molecule identification.
  • To assess the performance of the AutoBuild wizard across a diverse set of protein structures.

Main Methods:

Related Experiment Videos

  • Utilizing the PHENIX AutoBuild wizard, which integrates RESOLVE for model building and density modification with phenix.refine for structure refinement.
  • Implementing automated NCS detection and application during the iterative model building process.
  • Employing advanced model completion algorithms including loop building, chain crossovers, and side-chain optimization, alongside automated solvent picking.

    • Main Results:

    • The AutoBuild wizard was applied to 48 structures with resolutions from 1.1 to 3.2 Å.
    • Achieved a mean R-factor of 0.24 and a mean free R-factor of 0.29 across the tested structures.
    • Demonstrated that final model R-factor is primarily influenced by initial electron density quality, rather than resolution.

    Conclusions:

    • The PHENIX AutoBuild wizard significantly enhances automated model building and refinement efficiency.
    • The tool's advanced features enable robust structure completion and refinement, even with challenging datasets.
    • The performance of automated structure solution is strongly correlated with the quality of input electron density maps.