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7dgl redone
The Ni-bound dimeric structure of K78H/G80A/H82A myoglobin

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: 56.819 Å b: 63.276 Å c: 83.267 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 1.91 Å Reflections 23867 Test set 1191 (5.0%)
R 0.2090 R-free 0.2620
According to PDB-REDO
Resolution 1.91 Å Reflections 23867 Test set 1191 (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 0.2101 0.2119
R-free 0.2652 0.2544
Bond length RMS Z-score 0.714 0.432
Bond angle RMS Z-score 1.085 0.701
Model quality (raw scores | percentiles)
Ramachandran plot appearance -1.313 45 0.568 90
Rotamer normality -2.441 50 -2.176 55
Coarse packing 1.295 97 1.572 98
Fine packing 0.877 94 1.334 96
Bump severity 0.019 41 0.011 56
Hydrogen bond satisfaction 0.948 96 0.940 93
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 3
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 0
Residues fitting density worse 0
Change in density map fit (RSCC)