On macromolecular refinement at subatomic resolution with interatomic scatterers.
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.
Afonine
Pavel V
PV
Lawrence Berkeley National Laboratory, One Cyclotron Road, BLDG 64R0121, Berkeley, CA 94720, USA. pafonine@lbl.gov
Grosse-Kunstleve
Ralf W
RW
Adams
Paul D
PD
Lunin
Vladimir Y
VY
Urzhumtsev
Alexandre
A
D000818:Animals; D021343:Antifreeze Proteins, Type III; D018360:Crystallography, X-Ray / Q000379:methods; D008958:Models, Molecular; D009842:Oligopeptides / Q000737:chemistry*; D010740:Phospholipases / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*; D012604:Scorpion Venoms / Q000737:chemistry; D012984:Software; D014357:Trypsin / Q000737:chemistry
D021343:Antifreeze Proteins, Type III; D009842:Oligopeptides; D011506:Proteins; C092813:RD3 protein, eel; D012604:Scorpion Venoms; C044757:tyrosyl-glycyl-glycine; D010740:Phospholipases; D014357:Trypsin