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Gyre and gimble: a maximum-likelihood replacement for Patterson correlation refinement.

Airlie J McCoy1, Robert D Oeffner1, Claudia Millán2

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

The Phaser software

Keywords:
Patterson correlation refinementantibodiescrystallographic phasingfragment-based molecular replacementmaximum likelihood

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Area of Science:

  • Structural biology
  • Computational crystallography

Background:

  • Molecular replacement is a key technique in crystallography.
  • Accurate positioning of molecular models is crucial for successful structure solution.

Purpose of the Study:

  • To introduce and evaluate the maximum-likelihood gyre and gimble methods in Phaser.
  • To improve the refinement of rigid-body fragments in molecular replacement.

Main Methods:

  • Implementation of the maximum-likelihood gyre method for fragment orientation and positioning.
  • Application of the gimble method for post-positioning refinement.
  • Testing on the antibody Fab(26-10) dataset.

Main Results:

  • Gyre refinement successfully lowered root-mean-square atomic displacements.
  • Improved structure solution was achieved using ARCIMBOLDO_SHREDDER with gyre refinement.
  • The methods enhance the accuracy of rigid-body refinement in Phaser.

Conclusions:

  • The gyre and gimble methods provide effective strategies for rigid-body refinement.
  • These methods contribute to more robust and accurate molecular replacement solutions.
  • Phaser's capabilities are enhanced for structural biology applications.