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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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4d4u redone
Crystal Structure of Fucose binding lectin from Aspergillus Fumigatus (AFL) in complex with LewisY tetrasaccharide.

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

Crystallographic data
From PDB header
Spacegroup P 1 a: 47.317 Å b: 47.529 Å c: 77.365 Å α: 96.81° β: 100.24° γ: 113.61°
Resolution 1.99 Å Reflections 39130 Test set 1967 (5.0%)
R 0.1690 R-free 0.2200
According to PDB-REDO
Resolution 1.99 Å Reflections 39130 Test set 1967 (5.0%) 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 0.1707 0.1831
R-free 0.2201 0.2169
Bond length RMS Z-score 0.477 0.475
Bond angle RMS Z-score 0.677 0.698
Model quality (raw scores | percentiles)
Ramachandran plot appearance -1.064 51 -0.762 60
Rotamer normality -1.663 65 -0.794 81
Coarse packing 0.243 73 0.246 74
Fine packing -0.686 65 -0.758 62
Bump severity 0.003 82 0.004 78
Hydrogen bond satisfaction 0.935 90 0.930 87
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 9
Side chains flipped 3
Waters removed 28
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 0
Residues fitting density worse 0
Change in density map fit (RSCC)