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PDB-REDO Databank

The PDB-REDO databank contains optimised versions of existing PDB entries with electron density maps, a description of model changes, and a wealth of model validation data. It is a good starting point for any structural biology project.

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7jtv redone
Structure of IMPa from Pseudomonas aeruginosa in complex with an O-glycopeptide

This information was created with PDB-REDO version 7.34. Please log in to request an update.

Crystallographic data
From PDB header
Spacegroup P 1 21 1 a: 90.340 Å b: 156.500 Å c: 95.680 Å α: 90.00° β: 114.31° γ: 90.00°
Resolution 2.45 Å Reflections 88328 Test set 4347 (4.9%)
R 0.1800 R-free 0.2340
According to PDB-REDO
Resolution 2.45 Å Reflections 88328 Test set 4375 (5.0%) New test set, PDB-REDO compensated for this. Twin false
PDB-REDO files
Re-refined and rebuilt structure
( PDB | mmCIF | MTZ)
Re-refined (only) structure
( PDB | MTZ)
All files
PDBe RCSB PDB 3D bionotes Proteopedia
Validation metrics from PDB-REDO
Crystallographic refinement
R 0.2087 0.2097
R-free 0.2503 R-free was considered biased, the estimated unbiased R-free was used. 0.2434
Bond length RMS Z-score 0.344 0.547
Bond angle RMS Z-score 0.623 0.753
Model quality (raw scores | percentiles)
Ramachandran plot appearance -2.825 18 -2.521 22
Rotamer normality -3.530 32 -1.976 58
Coarse packing -0.428 40 -0.533 35
Fine packing -1.405 36 -1.349 38
Bump severity 0.008 64 0.005 74
Hydrogen bond satisfaction 0.901 52 0.902 53
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 25
Side chains flipped 4
Waters removed 41
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 0
Residues fitting density worse 0
Change in density map fit (RSCC)