Initiating heavy-atom-based phasing by multi-dimensional molecular replacement

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To obtain an electron-density map from a macromolecular crystal the phase problem needs to be solved, which often involves the use of heavy-atom derivative crystals and concomitant heavy-atom substructure determination. This is typically performed by dual-space methods, direct methods or Patterson-based approaches, which however may fail when only poorly diffracting derivative crystals are available. This is often the case for, for example, membrane proteins. Here, an approach for heavy-atom site identification based on a molecular-replacement parameter matrix (MRPM) is presented. It involves an n-dimensional search to test a wide spectrum of molecular-replacement parameters, such as different data sets and search models with different conformations. Results are scored by the ability to identify heavy-atom positions from anomalous difference Fourier maps. The strategy was successfully applied in the determination of a membrane-protein structure, the copper-transporting P-type ATPase CopA, when other methods had failed to determine the heavy-atom substructure. MRPM is well suited to proteins undergoing large conformational changes where multiple search models should be considered, and it enables the identification of weak but correct molecular-replacement solutions with maximum contrast to prime experimental phasing efforts.


  • Bjørn Panyella Pedersen
  • Pontus Gourdon
  • Xiangyu Liu
  • Jesper Lykkegaard Karlsen
  • Poul Nissen
Externa organisationer
  • Aarhus University


Sidor (från-till)440-5
Antal sidor6
TidskriftActa Crystallographica Section D: Structural Biology
Utgåva nummerPt 3
StatusPublished - 2016 mar
Peer review utfördJa
Externt publiceradJa