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PDB-REDO Databank

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4zs9 redone

This information was created with PDB-REDO version 7.32.

Crystallographic data
From PDB header
Spacegroup P 21 21 21 a: 55.540 Å b: 90.820 Å c: 146.750 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 1.37 Å Reflections 150939 Test set 7588 (5.0%)
R 0.1320 R-free 0.1670
According to PDB-REDO
Resolution 1.37 Å Reflections 150939 Test set 7584 (5.0%) New test set, PDB-REDO compensated for this. Twin false
PDB-REDO files
Re-refined and rebuilt structure
( PDB | mmCIF | MTZ)
Re-refined (only) structure
( PDB | MTZ)
YASARA scenes
(for visualisation of the results)
All files
PDBe RCSB PDB 3D bionotes Proteopedia
Validation metrics from PDB-REDO
Crystallographic refinement
R 0.1380 0.1254
R-free 0.1720 R-free was considered biased, the estimated unbiased R-free was used. 0.1609
Bond length RMS Z-score 0.566 0.671
Bond angle RMS Z-score 0.680 0.801
Model quality (raw scores | percentiles)
Ramachandran plot appearance 0.742 92 1.240 96
Rotamer normality 0.930 98 0.784 97
Coarse packing 0.830 91 0.809 91
Fine packing -0.935 56 -0.819 60
Bump severity 0.046 20 0.054 18
Hydrogen bond satisfaction 0.888 36 0.902 53
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 13
Side chains flipped 0
Waters removed 188
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 24
Residues fitting density worse 0
Change in density map fit (RSCC)