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PDB-REDO Databank

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4p25 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 1 a: 62.314 Å b: 63.124 Å c: 90.580 Å α: 72.80° β: 82.18° γ: 60.85°
Resolution 1.50 Å Reflections 170683 Test set 8552 (5.0%)
R 0.1340 R-free 0.1750
According to PDB-REDO
Resolution 1.50 Å Reflections 170683 Test set 8552 (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 0.1704 0.1545
R-free 0.1958 R-free was considered biased, the estimated unbiased R-free was used. 0.1771
Bond length RMS Z-score 0.285 0.738
Bond angle RMS Z-score 0.557 0.897
Model quality (raw scores | percentiles)
Ramachandran plot appearance -0.257 74 -0.159 76
Rotamer normality 0.919 98 0.398 95
Coarse packing -1.299 9 -1.368 8
Fine packing -1.250 42 -1.189 45
Bump severity 0.112 9 0.115 9
Hydrogen bond satisfaction 0.888 36 0.887 35
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 13
Side chains flipped 2
Waters removed 166
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 16
Residues fitting density worse 1
Change in density map fit (RSCC)