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Table 1 Chirality errors and cis peptide bonds in the Protein Data Bank

From: Stereochemical errors and their implications for molecular dynamics simulations

Method1 Chirality errors Cis peptide bonds
  Total 2 Residues per error 3 Structures analyzed 4 Structures with errors Total 2 Residues per cis bond 3 Structures analyzed 4 Structures with cis bonds
All 4047 9746 67942 648 (1%) 104455 368 65899 28576 (43%)
Electron microscopy 1273 529 201 40 (20%) 2316 262 192 93 (48%)
Solution NMR 280 2684 8444 105 (1%) 1289 565 7574 818 (11%)
X-ray diffraction 2494 15230 59147 503 (1%) 100776 368 57987 27646 (48%)
  1. 1 As given by EXPDTA record on each PDB file. Entries with more than one method were classified based on the first method listed. Only methods with at least 100 solved structures are shown in the table.
  2. 2 Total number of chirality errors or cis peptide bonds detected by the Chirality and Cispeptide VMD plugins, respectively.
  3. 3 Total number of residues divided by total number of chirality errors or cis peptide bonds. For chirality errors, all protein and nucleic acid residues are counted; for cis peptide bonds, only protein residues are counted.
  4. 4 For chirality, only structures containing at least one protein or nucleic acid residue were considered. For cis peptide bonds, only structures containing at least one peptide bond were kept in the analysis.