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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.

All the entries are treated with a consistent protocol that reduces the effects of differences in age, software, and depositors. This makes PDB-REDO a great datatset for large scale structure analysis studies.

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5o7u redone

This information was created with PDB-REDO version 7.36. Please log in to request an update.

Crystallographic data
From PDB header
Spacegroup F 2 3 a: 129.152 Å b: 129.152 Å c: 129.152 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 1.15 Å Reflections 63032 Test set 3140 (5.0%)
R 0.1040 R-free 0.1290
According to PDB-REDO
Resolution 1.15 Å Reflections 63032 Test set 3140 (5.0%) 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 0.1056 0.0985
R-free 0.1310 0.1251
Bond length RMS Z-score 0.514 0.618
Bond angle RMS Z-score 0.763 0.850
Model quality (raw scores | percentiles)
Ramachandran plot appearance 0.751 92 0.643 91
Rotamer normality 1.374 99 1.237 99
Coarse packing N/A N/A N/A N/A
Fine packing N/A N/A N/A N/A
Bump severity 0.451 2 0.472 2
Hydrogen bond satisfaction 0.761 3 0.792 4
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 4
Side chains flipped 0
Waters removed 39
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 6
Residues fitting density worse 1
Change in density map fit (RSCC)