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PDB-REDO Databank

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3leg redone
Lectin Domain of Lectinolysin complexed with Lewis Y Antigen

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

Crystallographic data
From PDB header
Spacegroup P 43 21 2 a: 67.060 Å b: 67.060 Å c: 98.670 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 2.01 Å Reflections 15565 Test set 791 (5.1%)
R 0.1930 R-free 0.2340
According to PDB-REDO
Resolution 2.01 Å Reflections 15565 Test set 791 (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 0.1889 0.1816
R-free 0.2224 0.2185
Bond length RMS Z-score 0.763 0.737
Bond angle RMS Z-score 0.761 0.835
Model quality (raw scores | percentiles)
Ramachandran plot appearance -0.521 67 -0.450 69
Rotamer normality -1.763 63 -1.032 77
Coarse packing 0.913 93 0.899 92
Fine packing -0.930 56 -0.854 59
Bump severity 0.208 5 0.189 6
Hydrogen bond satisfaction 0.917 73 0.914 70
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 7
Side chains flipped 0
Waters removed 0
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 0
Residues fitting density worse 0
Change in density map fit (RSCC)