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PDB-REDO Databank

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3wg4 redone
Crystal structure of Agrocybe cylindracea galectin mutant (N46A) with blood type A antigen tetraose

This information was created with PDB-REDO version 7.32. Please log in to request an update.

Crystallographic data
From PDB header
Spacegroup P 65 a: 102.824 Å b: 102.824 Å c: 74.578 Å α: 90.00° β: 90.00° γ: 120.00°
Resolution 1.60 Å Reflections 59060 Test set 2988 (5.1%)
R 0.1480 R-free 0.1750
According to PDB-REDO
Resolution 1.60 Å Reflections 59060 Test set 2988 (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 0.1485 0.1349
R-free 0.1736 0.1653
Bond length RMS Z-score 0.505 0.609
Bond angle RMS Z-score 0.625 0.788
Model quality (raw scores | percentiles)
Ramachandran plot appearance 0.239 85 0.266 85
Rotamer normality 0.502 96 0.274 95
Coarse packing 2.110 99 2.010 99
Fine packing 0.218 86 0.096 84
Bump severity 0.003 82 0.014 49
Hydrogen bond satisfaction 0.911 65 0.916 72
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 3
Side chains flipped 1
Waters removed 8
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 3
Residues fitting density worse 1
Change in density map fit (RSCC)