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3rpg redone
Bmi1/Ring1b-UbcH5c complex structure

This information was created with PDB-REDO version 7.0. Please log in to request an update.

Crystallographic data
From PDB header
Spacegroup P 32 2 1 a: 107.890 Å b: 107.890 Å c: 77.572 Å α: 90.00° β: 90.00° γ: 120.00°
Resolution 2.65 Å Reflections 15431 Test set 772 (5.0%)
R 0.2170 R-free 0.2430
According to PDB-REDO
Resolution 2.65 Å Reflections 15431 Test set 772 (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 0.2196 0.1850
R-free 0.2469 0.2511
Bond length RMS Z-score 0.204 0.544
Bond angle RMS Z-score 0.502 0.773
Model quality (raw scores | percentiles)
Ramachandran plot appearance -1.750 27 -1.318 36
Rotamer normality -3.242 19 -2.666 27
Coarse packing -0.535 N/A -0.532 N/A
Fine packing 0.273 90 0.387 91
Bump severity 0.039 35 0.002 96
Hydrogen bond satisfaction 0.900 50 0.899 49
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 3
Side chains flipped 0
Waters removed 3
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 50
Residues fitting density worse 0
Change in density map fit (RSCC)