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PDB-REDO Databank

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3lei redone
Lectin Domain of Lectinolysin complexed with Fucose

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: 97.800 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 1.90 Å Reflections 17956 Test set 916 (5.1%)
R 0.1990 R-free 0.2470
According to PDB-REDO
Resolution 1.90 Å Reflections 17956 Test set 916 (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 0.1977 0.1896
R-free 0.2405 0.2180
Bond length RMS Z-score 0.734 0.415
Bond angle RMS Z-score 0.753 0.664
Model quality (raw scores | percentiles)
Ramachandran plot appearance -0.619 64 -0.542 66
Rotamer normality -1.664 65 -0.905 79
Coarse packing 0.879 92 0.942 93
Fine packing -0.806 61 -0.580 68
Bump severity 0.039 23 0.001 92
Hydrogen bond satisfaction 0.905 57 0.920 77
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 8
Side chains flipped 0
Waters removed 2
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 0
Residues fitting density worse 0
Change in density map fit (RSCC)