On the interpretation and use of <|E|2>(d*) profiles

Acta Crystallogr D Biol Crystallogr. 2004 Feb;60(Pt 2):227-40. doi: 10.1107/S0907444903025538. Epub 2004 Jan 23.

Abstract

Profiles of squared normalized structure factors, <|E|(2)>(d*), have been computed for a large number of proteins and nucleic acids. These are interpreted in terms of their underlying structural features. It is also shown that the 'solvent dip' at around 6.3 A resolution is to a large extent a protein secondary-structure effect that is enhanced by the water structure. A hierarchical classification of protein structures based on their <|E|(2)>(d*) profiles is briefly outlined, together with the use of <|E|(2)>(d*) profiles as an improvement over Wilson absolute scale estimation and as a novel solvent-modelling method.

MeSH terms

  • Cluster Analysis
  • Crystallography, X-Ray / methods
  • Models, Statistical
  • Nucleic Acids / chemistry*
  • Protein Conformation
  • Protein Structure, Secondary
  • Proteins / chemistry*
  • Solvents / chemistry
  • Statistics as Topic / methods*
  • Water / chemistry

Substances

  • Nucleic Acids
  • Proteins
  • Solvents
  • Water