CheckMyMetal (CMM) Home CSGID Home Download archive for all four examples

Re-refinement statistics and geometry for selected metal-containing coordinates re-refined after CMM validation
(For details of the re-refinement, see Zheng et al. (submitted) Validating metal binding sites in macromolecule structures using the CheckMyMetal (CMM) web server)

PDB code (resolution) 3lkm (1.60Å) 2z08 (1.50Å) 1qy6 (1.90Å) 3lrk (1.95Å)
show below
show below
show below
show below
Download coordinate files: (link) (link) (pdb, mtz) (link) (link) (pdb, mtz) (link) (link) (pdb, mtz) (link) (link) (pdb, mtz)
R-factor (%)19.418.
Rfree (%) #22.420.717.124.522.820.423.021.117.8 *23.422.118.5
RMSD bond length (Å)0.0220.0060.0160.0320.0140.0170.0070.0430.0190.0100.0170.014
RMSD bond angle (°)
Clashscore **9.52 (67%)4.26 (97%)2.69
18.40 (17%)13.14 (41%)2.67
13.02 (62%)4.94 (97%)2.16
8.90 (85%)7.62 (90%)4.25
Rotamer outliers0.460.000.469.094.552.304.491.112.783.721.601.60
Ramachandran favored (%)96.6896.6898.3798.3299.16100.0097.6697.6698.1397.1197.5697.56
Molprobity score (2)1.711.421.062.492.131.332.191.371.332.071.661.45

# The Rfree set reported in the structure factor files available from the PDB were used for Rfree calculation.
* In the case of 1qy6, the structure factor set does not indicate excluded reflections for Rfree calculation set and the Rfree set was generated by HKL-3000 (3).
** Clashscore, rotamer outliers, and the number of residues in the Ramachandran plot favored regions were calculated using MolProbity (2)
Joosten,R.P. et al. (2012) Acta Cryst., D68, 484-496.
PDB_REDO: constructive validation, more than just looking for errors
Chen,V.B. et al. (2010) Acta Cryst., D66, 12-21.
MolProbity: all-atom structure validation for macromolecular crystallography
Minor,W. et al. (2006) Acta Cryst., D62, 859-886.
HKL-3000: the integration of data reduction and structure solution - from diffraction images to an initial model in minutes

Re-refined PDB coordinate (Download archive for all four examples: CMM-rerefined-examples.tar.gz)
Re-refined PDB coordinates will be shown here