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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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3io0 redone

This information was created with PDB-REDO version 7.0. Please log in to request an update.

Crystallographic data
From PDB header
Spacegroup I 21 3 a: 173.410 Å b: 173.410 Å c: 173.410 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 3.00 Å Reflections 17475 Test set 883 (5.1%)
R 0.1880 R-free 0.2030
According to PDB-REDO
Resolution 3.00 Å Reflections 17475 Test set 883 (5.1%) Twin false
PDB-REDO files
Re-refined and rebuilt structure
( PDB | mmCIF | MTZ)
Re-refined (only) structure
( PDB | MTZ)
YASARA scenes
(for visualisation of the results)
All files
PDBe RCSB PDB 3D bionotes Proteopedia
Validation metrics from PDB-REDO
Crystallographic refinement
R 0.1866 0.1691
R-free 0.2016 0.1829
Bond length RMS Z-score 0.516 0.579
Bond angle RMS Z-score 0.908 0.953
Model quality (raw scores | percentiles)
Ramachandran plot appearance -2.810 13 -2.101 21
Rotamer normality -5.912 1 -3.201 19
Coarse packing -0.196 N/A -0.071 N/A
Fine packing 0.109 87 0.595 93
Bump severity 0.036 38 0.016 66
Hydrogen bond satisfaction 0.854 19 0.876 31
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 5
Side chains flipped 0
Waters removed 0
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 17
Residues fitting density worse 1
Change in density map fit (RSCC)