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Related Experiment Videos

Optimizing Shake-and-Bake for proteins.

C M Weeks1, R Miller

  • 1Hauptman-Woodward Medical Research -Institute, Inc., 73 High Street, Buffalo, NY 14203, USA. weeks@hwi.buffalo.edu

Acta Crystallographica. Section D, Biological Crystallography
|March 25, 1999
PubMed
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Shake-and-Bake (SnB) is a direct-methods algorithm for solving protein structures. Parameter optimization is key for its successful application to large molecules, especially those lacking heavy atoms.

Area of Science:

  • Crystallography
  • Structural Biology
  • Computational Chemistry

Background:

  • Direct methods are crucial for ab initio structure determination.
  • Conventional direct methods have limitations with large molecules.
  • Shake-and-Bake (SnB) extends direct methods for protein structures.

Purpose of the Study:

  • To investigate the impact of parameter choices on SnB performance for protein structures.
  • To identify optimal parameters for SnB application to molecules up to 1000 non-H atoms.
  • To explore solvability enhancements for SnB in specific resolution ranges.

Main Methods:

  • Shake-and-Bake (SnB) algorithm applied to six protein structures.
  • Systematic variation of critical parameters: density modification peaks, phase refinement, refinement cycles.

Related Experiment Videos

  • Analysis of solvability at resolutions of 1.1 Å and 1.2–1.4 Å.

    • Main Results:

    • SnB successfully solved protein structures with up to 1000 non-H atoms.
    • Parameter choice significantly influences SnB performance.
    • Solvability at 1.2–1.4 Å resolution is enhanced by heavier atoms (S, Cl).
    • Increased refinement cycles and triplet phase invariants are needed for lower resolutions.

    Conclusions:

    • Shake-and-Bake is a powerful tool for ab initio protein structure determination.
    • Careful parameter selection is essential for successful SnB application.
    • Structural features like heavy atoms influence solvability at lower resolutions.