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7f71 redone
CRYSTAL STRUCTURE OF THE MYCOBACTERIUM TUBERCULOSIS L,D- TRANSPEPTIDASE-2 (LDTMT2) WITH PEPTIDOGLYCAN SUGAR MOIETY AND GLUTAMATE

This information was created with PDB-REDO version 7.37.

Crystallographic data
From PDB header
Spacegroup P 1 21 1 a: 60.906 Å b: 93.981 Å c: 75.539 Å α: 90.00° β: 92.97° γ: 90.00°
Resolution 1.58 Å Reflections 106008 Test set 2008 (1.9%)
R 0.1650 R-free 0.1980
According to PDB-REDO
Resolution 1.58 Å Reflections 106008 Test set 2008 (1.9%) Twin false
PDB-REDO files
Re-refined and rebuilt structure
( PDB | mmCIF | MTZ)
Re-refined (only) structure
( PDB | MTZ)
All files
(compressed)
Links
PDBe RCSB PDB 3D bionotes Proteopedia
Validation metrics from PDB-REDO
PDB PDB-REDO
Crystallographic refinement
R 0.1744 0.1332
R-free 0.2050 0.1758
Bond length RMS Z-score 0.395 0.616
Bond angle RMS Z-score 0.722 0.824
Model quality (raw scores | percentiles)
Ramachandran plot appearance -0.392 71 -0.112 78
Rotamer normality 0.067 93 1.072 98
Coarse packing -0.225 50 -0.124 55
Fine packing -1.194 45 -0.775 62
Bump severity 0.004 78 0.007 67
Hydrogen bond satisfaction 0.915 71 0.934 90
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 12
Side chains flipped 12
Waters removed 149
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 72
Residues fitting density worse 0
Change in density map fit (RSCC)