The Netherlands Cancer Institute
NWO logo
Johnson and Johnson logo
West-Life logo
iNEXT logo
Powered by
CCP4 logo
WHAT-IF logo
SDSC logo
3DNA logo
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.

Here you can find more information about downloading PDB-REDO databank entries. And here you can find the data usage license.

1uld redone
CGL2 in complex with blood group H type II

This information was created with PDB-REDO version 7.32. Please log in to request an update.

Crystallographic data
From PDB header
Spacegroup P 31 1 2 a: 113.613 Å b: 113.613 Å c: 122.329 Å α: 90.00° β: 90.00° γ: 120.00°
Resolution 2.10 Å Reflections 52686 Test set 2582 (4.9%)
R 0.2180 R-free 0.2470
According to PDB-REDO
Resolution 2.08 Å Reflections 52686 Test set 2582 (4.9%) 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 0.2131 0.1887
R-free 0.2349 0.2080
Bond length RMS Z-score 0.298 0.543
Bond angle RMS Z-score 0.663 0.778
Model quality (raw scores | percentiles)
Ramachandran plot appearance -2.127 27 -0.262 74
Rotamer normality -1.648 65 0.574 96
Coarse packing 0.574 85 0.631 87
Fine packing -0.203 78 0.030 83
Bump severity 0.012 53 0.005 74
Hydrogen bond satisfaction 0.928 85 0.935 90
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 15
Side chains flipped 0
Waters removed 27
Peptides flipped 1
Chiralities fixed 0
Residues fitting density better 6
Residues fitting density worse 0
Change in density map fit (RSCC)