On macromolecular refinement at subatomic resolution with interatomic scatterers

Acta Crystallogr D Biol Crystallogr. 2007 Nov;63(Pt 11):1194-7. doi: 10.1107/S0907444907046148. Epub 2007 Oct 17.


A study of the accurate electron-density distribution in molecular crystals at subatomic resolution (better than approximately 1.0 A) requires more detailed models than those based on independent spherical atoms. A tool that is conventionally used in small-molecule crystallography is the multipolar model. Even at upper resolution limits of 0.8-1.0 A, the number of experimental data is insufficient for full multipolar model refinement. As an alternative, a simpler model composed of conventional independent spherical atoms augmented by additional scatterers to model bonding effects has been proposed. Refinement of these mixed models for several benchmark data sets gave results that were comparable in quality with the results of multipolar refinement and superior to those for conventional models. Applications to several data sets of both small molecules and macromolecules are shown. These refinements were performed using the general-purpose macromolecular refinement module phenix.refine of the PHENIX package.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Antifreeze Proteins, Type III
  • Crystallography, X-Ray / methods
  • Models, Molecular*
  • Oligopeptides / chemistry*
  • Phospholipases / chemistry
  • Proteins / chemistry*
  • Scorpion Venoms / chemistry
  • Software
  • Trypsin / chemistry


  • Antifreeze Proteins, Type III
  • Oligopeptides
  • Proteins
  • RD3 protein, eel
  • Scorpion Venoms
  • tyrosyl-glycyl-glycine
  • Phospholipases
  • Trypsin