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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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5ajb redone

This information was created with PDB-REDO version 7.31. Please log in to request an update.

Crystallographic data
From PDB header
Spacegroup P 21 21 21 a: 43.185 Å b: 58.630 Å c: 106.713 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 1.80 Å Reflections 25579 Test set 1304 (5.1%)
R 0.1460 R-free 0.1800
According to PDB-REDO
Resolution 1.80 Å Reflections 25579 Test set 1304 (5.1%) 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 0.1453 0.1424
R-free 0.1802 0.1773
Bond length RMS Z-score 0.699 0.705
Bond angle RMS Z-score 0.767 0.776
Model quality (raw scores | percentiles)
Ramachandran plot appearance 0.351 87 0.392 87
Rotamer normality 0.868 98 0.857 98
Coarse packing 1.325 97 1.140 96
Fine packing -2.721 3 -2.625 4
Bump severity 0.472 2 0.474 2
Hydrogen bond satisfaction 0.885 33 0.875 25
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 4
Side chains flipped 3
Waters removed 4
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 0
Residues fitting density worse 0
Change in density map fit (RSCC)