Hosting
The Netherlands Cancer Institute
Funding
NWO logo
Johnson and Johnson logo
West-Life logo
iNEXT logo
Powered by
CCP4 logo
WHAT-IF logo
SDSC logo
YASARA 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.

4gwj redone
His 62 mutant of the lectin binding domain of Lectinolysin complexed with Lewis b

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

Crystallographic data
From PDB header
Spacegroup P 43 21 2 a: 66.923 Å b: 66.923 Å c: 99.387 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 1.60 Å Reflections 29456 Test set 1499 (5.1%)
R 0.1790 R-free 0.2100
According to PDB-REDO
Resolution 1.60 Å Reflections 29456 Test set 1499 (5.1%) Twin false
PDB-REDO files
Re-refined and rebuilt structure
( PDB | mmCIF | MTZ)
Re-refined (only) structure
( PDB | MTZ)
All files
(compressed)
Links
PDBe RCSB PDB 3D bionotes Proteopedia
Validation metrics from PDB-REDO
PDB PDB-REDO
Crystallographic refinement
R 0.1751 0.1436
R-free 0.2039 0.1789
Bond length RMS Z-score 1.407 0.734
Bond angle RMS Z-score 1.353 0.820
Model quality (raw scores | percentiles)
Ramachandran plot appearance -0.309 73 0.462 88
Rotamer normality -0.337 88 0.615 97
Coarse packing 0.967 94 1.027 94
Fine packing -1.124 48 -0.732 63
Bump severity 0.217 5 0.201 5
Hydrogen bond satisfaction 0.895 44 0.920 77
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 8
Side chains flipped 0
Waters removed 20
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 18
Residues fitting density worse 0
Change in density map fit (RSCC)