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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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6hjd redone

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

Crystallographic data
From PDB header
Spacegroup P 21 21 21 a: 82.965 Å b: 108.291 Å c: 115.621 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 1.54 Å Reflections 153804 Test set 7676 (5.0%)
R 0.1930 R-free 0.2240
According to PDB-REDO
Resolution 1.54 Å Reflections 153804 Test set 7676 (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 0.1919 0.1900
R-free 0.2223 0.2169
Bond length RMS Z-score 0.784 0.670
Bond angle RMS Z-score 0.989 0.817
Model quality (raw scores | percentiles)
Ramachandran plot appearance -0.395 70 0.498 89
Rotamer normality -1.203 74 -0.150 90
Coarse packing 1.138 96 1.158 96
Fine packing 0.229 86 0.391 89
Bump severity 0.030 29 0.039 23
Hydrogen bond satisfaction 0.880 28 0.884 32
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 12
Side chains flipped 0
Waters removed 1
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 17
Residues fitting density worse 1
Change in density map fit (RSCC)