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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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1dwt redone
Photorelaxed horse heart MYOGLOBIN CO complex

This information was created with PDB-REDO version 7.28. Please log in to request an update.

Crystallographic data
From PDB header
Spacegroup P 1 21 1 a: 62.800 Å b: 28.800 Å c: 35.200 Å α: 90.00° β: 106.20° γ: 90.00°
Resolution 1.40 Å Reflections 23665 Test set 1502 (6.3%)
R 0.1970 R-free 0.2430
According to PDB-REDO
Resolution 1.40 Å Reflections 23665 Test set 1502 (6.3%) 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 0.1890 0.1531
R-free 0.2287 0.1829
Bond length RMS Z-score 0.339 0.703
Bond angle RMS Z-score 0.654 1.042
Model quality (raw scores | percentiles)
Ramachandran plot appearance 0.553 89 0.218 84
Rotamer normality -3.151 37 -1.775 62
Coarse packing 1.210 96 1.036 94
Fine packing 0.147 85 0.196 86
Bump severity 0.004 78 0.011 56
Hydrogen bond satisfaction 0.936 91 0.944 95
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 6
Side chains flipped 0
Waters removed 8
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 15
Residues fitting density worse 0
Change in density map fit (RSCC)