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Related Experiment Videos

Shake-and-Bake applications using simulated reference-beam data for crambin.

C M Weeks1, H Xu, H A Hauptman

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

Acta Crystallographica. Section A, Foundations of Crystallography
|June 14, 2000
PubMed
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The Shake-and-Bake method successfully determined protein phases from simulated data, even with significant errors. This indicates direct methods can aid crystallographic phasing at lower resolutions.

Area of Science:

  • Crystallography
  • Structural Biology
  • Computational Chemistry

Background:

  • Accurate phase determination is crucial for solving protein structures using X-ray crystallography.
  • Direct methods offer an alternative to traditional phasing techniques, but their application at lower resolutions is challenging.

Purpose of the Study:

  • To evaluate the efficacy of the Shake-and-Bake method with reference-beam data for protein phase determination.
  • To assess the impact of phase errors on the success of the Shake-and-Bake method across various resolutions.

Main Methods:

  • Application of the Shake-and-Bake (SnB) algorithm to simulated reference-beam data of the protein crambin.
  • Generation of triplet invariants with simulated mean triplet-phase errors ranging from 0 to 60 degrees.

Related Experiment Videos

  • Analysis of phase determination success at resolutions from 1.5 to 3.0 Å.

    • Main Results:

    • The Shake-and-Bake method successfully identified trial phase sets with mean errors of 40-45 degrees when input phase errors were up to 40 degrees.
    • Accurate phasing was achieved at 1.5 Å resolution using a single reference-beam dataset.
    • Peak picking provided valuable phase constraints even at the lowest tested resolution (3.0 Å).

    Conclusions:

    • The Shake-and-Bake method, combined with reference-beam data, shows promise for macromolecular phasing.
    • Direct methods may be applicable to crystallographic data at resolutions lower than previously thought feasible.
    • Further investigation into reference-beam assisted direct methods could expand their utility in structural biology.