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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)
PDBPDB-REDO(1)Re-refined:
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PDBPDB-REDO(1)Re-refined:
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PDBPDB-REDO(1)Re-refined:
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PDBPDB-REDO(1)Re-refined:
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Download coordinate files: (link) (link) (pdb, mtz) (link) (link) (pdb, mtz) (link) (link) (pdb, mtz) (link) (link) (pdb, mtz)
R-factor (%)19.418.214.220.119.317.220.018.014.220.418.414.6
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 (°)2.01.31.92.91.72.1N/A2.11.71.41.81.7
Clashscore **9.52 (67%)4.26 (97%)2.69
(99%)
18.40 (17%)13.14 (41%)2.67
(99%)
13.02 (62%)4.94 (97%)2.16
(99%)
8.90 (85%)7.62 (90%)4.25
(98%)
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)
1.
 
Joosten,R.P. et al. (2012) Acta Cryst., D68, 484-496.
PDB_REDO: constructive validation, more than just looking for errors
2.
 
Chen,V.B. et al. (2010) Acta Cryst., D66, 12-21.
MolProbity: all-atom structure validation for macromolecular crystallography
3.
 
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