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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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4fnu redone

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

Crystallographic data
From PDB header
Spacegroup P 32 2 1 a: 154.070 Å b: 154.070 Å c: 238.020 Å α: 90.00° β: 90.00° γ: 120.00°
Resolution 3.60 Å Reflections 38121 Test set 1906 (5.0%)
R 0.2380 R-free 0.2820
According to PDB-REDO
Resolution 3.60 Å Reflections 38121 Test set 1906 (5.0%) 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 0.2578 0.2122
R-free 0.2965 0.2411
Bond length RMS Z-score 0.180 0.386
Bond angle RMS Z-score 0.432 0.719
Model quality (raw scores | percentiles)
Ramachandran plot appearance -2.550 21 -3.503 12
Rotamer normality -3.422 33 -4.708 18
Coarse packing -0.996 16 -0.643 29
Fine packing -2.466 6 -1.687 24
Bump severity 0.089 11 0.071 14
Hydrogen bond satisfaction 0.790 4 0.805 6
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 12
Side chains flipped 0
Waters removed 0
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 50
Residues fitting density worse 0
Change in density map fit (RSCC)