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.

2frs redone
Crystal structure of the f15w mutant of apo-cellular retinoic acid binding protein type ii at 1.51 angstroms resolution

This information was created with PDB-REDO version 7.36. Please log in to request an update.

Crystallographic data
From PDB header
Spacegroup P 1 a: 34.582 Å b: 37.030 Å c: 58.693 Å α: 102.00° β: 106.12° γ: 93.00°
Resolution 1.51 Å Reflections 39495 Test set 3946 (10.0%)
R 0.1740 R-free 0.2400
According to PDB-REDO
Resolution 1.51 Å Reflections 39495 Test set 3946 (10.0%) 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 0.1766 0.1827
R-free 0.2440 0.2301
Bond length RMS Z-score 0.640 0.478
Bond angle RMS Z-score 0.778 0.707
Model quality (raw scores | percentiles)
Ramachandran plot appearance 1.282 96 1.646 97
Rotamer normality -2.187 54 -1.341 71
Coarse packing 1.096 95 1.322 97
Fine packing 1.534 97 2.504 99
Bump severity 0.066 15 0.025 34
Hydrogen bond satisfaction 0.935 90 0.947 96
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 4
Side chains flipped 12
Waters removed 45
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 2
Residues fitting density worse 0
Change in density map fit (RSCC)