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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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6p4q redone
Salmonella typhi PltB Homopentamer N29K Mutant with Neu5Ac-alpha-2-3-Gal-beta-1-4-GlcNAc Glycans

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

Crystallographic data
From PDB header
Spacegroup P 21 21 21 a: 61.053 Å b: 96.894 Å c: 119.006 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 1.77 Å Reflections 69142 Test set 2000 (2.9%)
R 0.1800 R-free 0.2030
According to PDB-REDO
Resolution 1.77 Å Reflections 69142 Test set 2000 (2.9%) 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 0.1818 0.1778
R-free 0.2023 0.1935
Bond length RMS Z-score 0.349 0.703
Bond angle RMS Z-score 0.647 0.833
Model quality (raw scores | percentiles)
Ramachandran plot appearance -0.333 72 -0.080 78
Rotamer normality -0.382 87 -0.045 92
Coarse packing 1.061 95 0.974 94
Fine packing -1.324 39 -1.353 38
Bump severity 0.008 64 0.006 70
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 3
Side chains flipped 0
Waters removed 0
Peptides flipped 1
Chiralities fixed 0
Residues fitting density better 1
Residues fitting density worse 0
Change in density map fit (RSCC)