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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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6wmo redone
Human poly-N-acetyl-lactosamine synthase structure demonstrates a modular assembly of catalytic subsites for GT-A glycosyltransferases

This information was created with PDB-REDO version 7.34. Please log in to request an update.

Crystallographic data
From PDB header
Spacegroup P 21 21 21 a: 48.190 Å b: 109.280 Å c: 147.550 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 1.85 Å Reflections 67312 Test set 3367 (5.0%)
R 0.1830 R-free 0.2120
According to PDB-REDO
Resolution 1.85 Å Reflections 67312 Test set 3367 (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 0.1896 0.1968
R-free 0.2095 0.2152
Bond length RMS Z-score 0.329 0.540
Bond angle RMS Z-score 0.666 0.792
Model quality (raw scores | percentiles)
Ramachandran plot appearance -0.130 77 -0.393 71
Rotamer normality -0.531 85 -0.847 80
Coarse packing 0.068 65 0.091 66
Fine packing -1.232 43 -1.117 48
Bump severity 0.398 2 0.209 5
Hydrogen bond satisfaction 0.883 31 0.888 36
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 20
Side chains flipped 0
Waters removed 21
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 5
Residues fitting density worse 1
Change in density map fit (RSCC)