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PDB-REDO Databank

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3lek redone
Lectin Domain of Lectinolysin complexed with Lewis B 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: 67.010 Å b: 67.010 Å c: 97.650 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 2.00 Å Reflections 15595 Test set 787 (5.0%)
R 0.2020 R-free 0.2370
According to PDB-REDO
Resolution 2.00 Å Reflections 15595 Test set 787 (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 0.1955 0.1895
R-free 0.2362 0.2214
Bond length RMS Z-score 0.718 0.640
Bond angle RMS Z-score 0.728 0.777
Model quality (raw scores | percentiles)
Ramachandran plot appearance 0.180 84 0.023 81
Rotamer normality -1.864 61 -1.652 65
Coarse packing 1.002 94 0.984 94
Fine packing -0.802 61 -0.677 65
Bump severity 0.005 74 0.001 92
Hydrogen bond satisfaction 0.900 50 0.896 45
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 6
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)