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PDB-REDO Databank

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5elc redone
Cholera toxin El Tor B-pentamer in complex with Lewis-y

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 21 1 a: 63.667 Å b: 80.916 Å c: 95.770 Å α: 90.00° β: 96.07° γ: 90.00°
Resolution 1.50 Å Reflections 146071 Test set 7329 (5.0%)
R 0.2210 R-free 0.2600
According to PDB-REDO
Resolution 1.50 Å Reflections 146071 Test set 7329 (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 0.2191 0.2248
R-free 0.2566 0.2488
Bond length RMS Z-score 0.701 0.514
Bond angle RMS Z-score 0.882 0.735
Model quality (raw scores | percentiles)
Ramachandran plot appearance -0.931 55 0.813 92
Rotamer normality -1.965 59 -0.326 88
Coarse packing 1.340 97 1.439 98
Fine packing 0.087 84 0.390 89
Bump severity 0.393 2 0.065 15
Hydrogen bond satisfaction 0.873 23 0.878 27
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 31
Side chains flipped 0
Waters removed 15
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 0
Residues fitting density worse 4
Change in density map fit (RSCC)