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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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7oih redone
Glycosylation in the crystal structure of neutrophil myeloperoxidase

This information was created with PDB-REDO version 8.0.

Crystallographic data
From PDB header
Spacegroup C 1 2 1 a: 155.910 Å b: 144.634 Å c: 236.454 Å α: 90.00° β: 91.53° γ: 90.00°
Resolution 2.60 Å Reflections 143788 Test set 1826 (1.3%)
R 0.1788 R-free 0.2195
According to PDB-REDO
Resolution 2.60 Å Reflections 143788 Test set 1826 (1.3%) 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 0.1636 0.1902
R-free 0.2101 0.2239
Bond length RMS Z-score 0.428 0.399
Bond angle RMS Z-score 0.808 0.653
Model quality (raw scores | percentiles)
Ramachandran plot appearance -2.280 25 -1.896 32
Rotamer normality -1.667 64 -0.967 78
Coarse packing -0.965 17 -1.025 15
Fine packing -2.330 8 -2.254 9
Bump severity 0.470 2 0.430 2
Hydrogen bond satisfaction 0.881 29 0.863 18
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 71
Side chains flipped 0
Waters removed 721
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 1
Residues fitting density worse 38
Change in density map fit (RSCC)