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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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2ox9 redone

This information was created with PDB-REDO version 7.0. Please log in to request an update.

Crystallographic data
From PDB header
Spacegroup P 1 a: 47.998 Å b: 53.755 Å c: 59.084 Å α: 67.75° β: 76.70° γ: 85.37°
Resolution 1.95 Å Reflections 35627 Test set 1785 (5.0%)
R 0.2240 R-free 0.2730
According to PDB-REDO
Resolution 1.95 Å Reflections 35627 Test set 1785 (5.0%) Twin false
PDB-REDO files
Re-refined and rebuilt structure
( PDB | mmCIF | MTZ)
Re-refined (only) structure
( PDB | MTZ)
YASARA scenes
(for visualisation of the results)
All files
PDBe RCSB PDB 3D bionotes Proteopedia
Validation metrics from PDB-REDO
Crystallographic refinement
R 0.2214 0.1800
R-free 0.2679 0.2139
Bond length RMS Z-score 0.283 0.940
Bond angle RMS Z-score 0.641 0.966
Model quality (raw scores | percentiles)
Ramachandran plot appearance -1.948 23 0.258 83
Rotamer normality -3.342 17 -0.958 65
Coarse packing -0.423 N/A -0.181 N/A
Fine packing -3.024 1 -2.600 3
Bump severity 0.210 4 0.195 5
Hydrogen bond satisfaction 0.850 17 0.847 16
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 9
Side chains flipped 0
Waters removed 26
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 145
Residues fitting density worse 0
Change in density map fit (RSCC)