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.

6cbp redone
Crystal structure of the single chain variable fragment of the DH270.6 bnAb in complex with the Man9-V3 glycopeptide

This information was created with PDB-REDO version 7.31. Please log in to request an update.

Crystallographic data
From PDB header
Spacegroup P 41 2 2 a: 68.005 Å b: 68.005 Å c: 128.835 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 2.17 Å Reflections 15873 Test set 813 (5.1%)
R 0.2210 R-free 0.2780
According to PDB-REDO
Resolution 2.17 Å Reflections 15873 Test set 813 (5.1%) 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 0.2448 0.2186
R-free 0.2896 0.2705
Bond length RMS Z-score 0.272 0.709
Bond angle RMS Z-score 0.495 0.897
Model quality (raw scores | percentiles)
Ramachandran plot appearance -0.994 53 -1.469 41
Rotamer normality -0.663 83 -2.636 46
Coarse packing -0.977 17 -1.008 16
Fine packing -1.048 51 -0.967 54
Bump severity 0.390 2 0.549 1
Hydrogen bond satisfaction 0.868 20 0.885 33
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 5
Side chains flipped 1
Waters removed 3
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 4
Residues fitting density worse 0
Change in density map fit (RSCC)