Completeness of NOEs in protein structure: a statistical analysis of NMR.
The completeness of experimentally observed NOE restraints of a set of 97 NMR protein structures deposited in the PDB has been assessed. Completeness is defined as the ratio of the number of experimentally observed NOEs and the number of 'expected NOEs'. A practical definition of 'expected NOEs' based on inter-proton distances in the structures up to a given cut-off distance is proposed. The average completeness for the set of 97 structures is 68, 48, and 26% up to 3, 4, and 5 A cut-off distances, respectively. For recent state-of-the-art structures these numbers are approximately 90, 75, and 45%. Almost 20% of the observed NOEs are between atoms that are further than 5 A apart in the final structures. The completeness is independent of the relative surface accessibility and does not depend strongly on residue type, secondary structure or local precision, although the number of observed NOEs in these classes varies considerably. The completeness of NOE restraints is a useful quality criterion in the course of structure refinement. The completeness per residue is more informative than the number of NOEs per residue, which makes it a useful tool to assess the quality of the NMR data set in relation to the resulting structures.
Doreleijers
J F
JF
Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands.
Raves
M L
ML
Rullmann
T
T
Kaptein
R
R
D000595:Amino Acid Sequence; D000596:Amino Acids; D001426:Bacterial Proteins / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D016208:Databases, Factual; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D019151:Peptide Library; D014157:Transcription Factors / Q000737:chemistry
D000596:Amino Acids; D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D019151:Peptide Library; D014157:Transcription Factors; C040330:histone-like protein HU, bacteria