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.

5wjq redone

This information was created with PDB-REDO version 7.37. Please log in to request an update.

Crystallographic data
From PDB header
Spacegroup P 21 21 2 a: 180.641 Å b: 35.239 Å c: 81.912 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 2.79 Å Reflections 13698 Test set 685 (5.0%)
R 0.1930 R-free 0.2630
According to PDB-REDO
Resolution 2.79 Å Reflections 13698 Test set 685 (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 0.2203 0.2645
R-free 0.2792 0.3236
Bond length RMS Z-score 0.765 0.566
Bond angle RMS Z-score 0.894 0.817
Model quality (raw scores | percentiles)
Ramachandran plot appearance -4.028 9 -4.627 6
Rotamer normality -6.593 6 -4.293 22
Coarse packing N/A N/A -3.421 0
Fine packing N/A N/A -3.680 1
Dinucleotide conformation (CONFAL) 47.1 52 56.2 72
Base pair conformation 1.7 56 1.1 83
Bump severity 0.142 8 0.053 18
Hydrogen bond satisfaction 0.710 1 0.712 1
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 6
Side chains flipped 32
Waters removed 20
Peptides flipped 5
Chiralities fixed 0
Residues fitting density better 2
Residues fitting density worse 3
Change in density map fit (RSCC)