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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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5o7v redone

This information was created with PDB-REDO version 7.36. Please log in to request an update.

Crystallographic data
From PDB header
Spacegroup F 2 3 a: 129.883 Å b: 129.883 Å c: 129.883 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 1.28 Å Reflections 46835 Test set 2369 (5.1%)
R 0.1220 R-free 0.1480
According to PDB-REDO
Resolution 1.28 Å Reflections 46835 Test set 2369 (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 0.1233 0.1165
R-free 0.1490 0.1467
Bond length RMS Z-score 0.634 0.713
Bond angle RMS Z-score 0.823 0.894
Model quality (raw scores | percentiles)
Ramachandran plot appearance -0.035 79 0.058 81
Rotamer normality -0.012 92 0.129 93
Coarse packing -1.296 9 -1.135 12
Fine packing -3.627 1 -3.631 1
Bump severity 0.503 1 0.491 2
Hydrogen bond satisfaction 0.799 5 0.788 4
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 16
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 1
Residues fitting density worse 1
Change in density map fit (RSCC)