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.

4gzj redone
Active-site mutant of potato endo-1,3-beta-glucanase in complex with laminaratriose and laminaratetrose

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

Crystallographic data
From PDB header
Spacegroup P 1 21 1 a: 55.307 Å b: 49.202 Å c: 57.431 Å α: 90.00° β: 98.84° γ: 90.00°
Resolution 1.55 Å Reflections 44352 Test set 1139 (2.6%)
R 0.1510 R-free 0.1810
According to PDB-REDO
Resolution 1.55 Å Reflections 44352 Test set 1139 (2.6%) 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 0.1529 0.1673
R-free 0.1816 0.1948
Bond length RMS Z-score 0.738 0.726
Bond angle RMS Z-score 0.820 0.843
Model quality (raw scores | percentiles)
Ramachandran plot appearance -0.164 76 -0.347 72
Rotamer normality 0.821 98 0.550 96
Coarse packing -0.221 50 -0.260 48
Fine packing -2.337 8 -2.333 8
Bump severity 0.003 82 0.003 82
Hydrogen bond satisfaction 0.890 38 0.891 39
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 9
Side chains flipped 0
Waters removed 1
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 0
Residues fitting density worse 0
Change in density map fit (RSCC)