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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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4gzi redone
Active-site mutant of potato endo-1,3-beta-glucanase in complex with laminaratriose

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

Crystallographic data
From PDB header
Spacegroup P 1 21 1 a: 54.895 Å b: 49.273 Å c: 57.075 Å α: 90.00° β: 98.38° γ: 90.00°
Resolution 1.68 Å Reflections 34202 Test set 1076 (3.1%)
R 0.1360 R-free 0.1710
According to PDB-REDO
Resolution 1.68 Å Reflections 34202 Test set 1076 (3.1%) 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 0.1390 0.1380
R-free 0.1742 0.1713
Bond length RMS Z-score 0.726 0.734
Bond angle RMS Z-score 0.786 0.839
Model quality (raw scores | percentiles)
Ramachandran plot appearance -0.647 63 -0.567 66
Rotamer normality 1.101 98 1.098 98
Coarse packing -0.321 45 -0.333 44
Fine packing -2.179 10 -2.230 9
Bump severity 0.002 87 0.001 92
Hydrogen bond satisfaction 0.910 64 0.890 38
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 7
Side chains flipped 0
Waters removed 8
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 2
Residues fitting density worse 0
Change in density map fit (RSCC)