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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.

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3uet redone
Crystal structure of alpha-1,3/4-fucosidase from Bifidobacterium longum subsp. infantis D172A/E217A mutant complexed with lacto-N-fucopentaose II

This information was created with PDB-REDO version 7.33. Please log in to request an update.

Crystallographic data
From PDB header
Spacegroup P 21 21 21 a: 82.588 Å b: 105.971 Å c: 120.715 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 2.10 Å Reflections 60159 Test set 3047 (5.1%)
R 0.1730 R-free 0.2230
According to PDB-REDO
Resolution 2.10 Å Reflections 60159 Test set 3047 (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 0.1744 0.1742
R-free 0.2199 0.2003
Bond length RMS Z-score 1.013 0.482
Bond angle RMS Z-score 0.994 0.722
Model quality (raw scores | percentiles)
Ramachandran plot appearance -1.957 30 -0.831 58
Rotamer normality -2.688 45 -1.157 74
Coarse packing -0.591 32 -0.503 36
Fine packing -1.617 27 -1.458 33
Bump severity 0.034 26 0.045 21
Hydrogen bond satisfaction 0.898 48 0.891 39
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 15
Side chains flipped 0
Waters removed 9
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 0
Residues fitting density worse 0
Change in density map fit (RSCC)