Jove
Visualize
Contact Us

Related Experiment Videos

Solving structures of protein complexes by molecular replacement with Phaser.

Airlie J McCoy1

  • 1University of Cambridge, Department of Haematology, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 2XY, England. ajm201@cam.ac.uk

Acta Crystallographica. Section D, Biological Crystallography
|December 14, 2006
PubMed
Summary

Molecular replacement (MR) struggles with complex structures. Phaser's automated method, using maximum-likelihood, improves solving difficult molecular replacement problems by building models component by component.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Scotty: lattice coincidences for macromolecular crystallographic phasing.

Acta crystallographica. Section D, Structural biology·2026
Same author

Scotty: lattice coincidences in the Protein Data Bank.

Acta crystallographica. Section D, Structural biology·2026
Same author

AlphaFold as a prior: experimental structure determination conditioned on a pretrained neural network.

Nature methods·2026
Same author

Xtricorder: a likelihood-enhanced self-rotation function and application to a machine learning-enhanced Matthews prediction of asymmetric unit copy number.

Acta crystallographica. Section D, Structural biology·2025
Same author

AlphaFold as a Prior: Experimental Structure Determination Conditioned on a Pretrained Neural Network.

bioRxiv : the preprint server for biology·2025
Same author

Likelihood-based interactive local docking into cryo-EM maps in ChimeraX.

Acta crystallographica. Section D, Structural biology·2024
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Area of Science:

  • Structural biology
  • Crystallography

Background:

  • Molecular replacement (MR) is a crucial technique in crystallography for determining protein structures.
  • The difficulty of MR increases with the number of components in the asymmetric unit, especially when individual components contribute little to the overall signal.

Purpose of the Study:

  • To describe and illustrate the application of maximum-likelihood-based MR methods for solving complex structures.
  • To present strategies for optimizing the automated MR search procedure in Phaser for challenging cases.

Main Methods:

  • Utilizing maximum-likelihood MR functions within a 'tree search with pruning' approach.
  • Employing the automated search procedure in the program Phaser.

Main Results:

Related Experiment Videos

  • Phaser's automated MR has successfully solved many previously intractable problems.
  • Specific case studies demonstrate optimal use and necessary modifications for problematic scenarios, such as high copy numbers or varying B-factors.

    • Conclusions:

    • Maximum-likelihood MR, as implemented in Phaser, offers a robust solution for complex molecular replacement challenges.
    • Adapting automated search strategies is key to overcoming difficulties in specific structural biology cases.