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PDB-REDO Databank

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4gwi redone
His 62 mutant of the lectin binding domain of lectinolysin complexed 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 43 21 2 a: 67.097 Å b: 67.097 Å c: 99.432 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 1.60 Å Reflections 30495 Test set 1536 (5.0%)
R 0.1680 R-free 0.1900
According to PDB-REDO
Resolution 1.60 Å Reflections 30495 Test set 1536 (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 0.1626 0.1278
R-free 0.1764 0.1479
Bond length RMS Z-score 1.319 0.756
Bond angle RMS Z-score 1.254 0.831
Model quality (raw scores | percentiles)
Ramachandran plot appearance 0.561 90 0.847 93
Rotamer normality 0.567 96 0.776 97
Coarse packing 0.794 90 0.717 89
Fine packing -0.917 56 -0.620 67
Bump severity 0.275 4 0.207 5
Hydrogen bond satisfaction 0.911 65 0.904 56
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 5
Side chains flipped 0
Waters removed 9
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 20
Residues fitting density worse 0
Change in density map fit (RSCC)