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.

4d72 redone
Crystal structure of a family 98 glycoside hydrolase catalytic module (Sp3GH98) in complex with the type 2 blood group A-tetrasaccharide (E558A L19 mutant)

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

Crystallographic data
From PDB header
Spacegroup C 2 2 21 a: 92.250 Å b: 154.420 Å c: 97.080 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 2.11 Å Reflections 40022 Test set 2009 (5.0%)
R 0.1680 R-free 0.2060
According to PDB-REDO
Resolution 2.11 Å Reflections 40022 Test set 2009 (5.0%) 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 0.1684 0.1618
R-free 0.2016 0.2000
Bond length RMS Z-score 0.469 0.417
Bond angle RMS Z-score 0.617 0.675
Model quality (raw scores | percentiles)
Ramachandran plot appearance -1.405 42 -1.313 45
Rotamer normality -1.006 77 -0.539 85
Coarse packing -0.181 52 -0.171 53
Fine packing -2.120 11 -1.815 20
Bump severity 0.003 82 0.003 82
Hydrogen bond satisfaction 0.897 46 0.883 31
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 30
Side chains flipped 5
Waters removed 10
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 0
Residues fitting density worse 0
Change in density map fit (RSCC)