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3wg3 redone
Crystal structure of Agrocybe cylindracea galectin 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: 102.921 Å b: 102.921 Å c: 74.694 Å α: 90.00° β: 90.00° γ: 120.00°
Resolution 1.35 Å Reflections 98506 Test set 4914 (5.0%)
R 0.1400 R-free 0.1560
According to PDB-REDO
Resolution 1.35 Å Reflections 98506 Test set 4914 (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 0.1368 0.1180
R-free 0.1525 0.1379
Bond length RMS Z-score 0.405 0.646
Bond angle RMS Z-score 0.593 0.828
Model quality (raw scores | percentiles)
Ramachandran plot appearance 0.257 85 0.303 86
Rotamer normality 0.190 94 0.315 95
Coarse packing 2.006 99 1.987 99
Fine packing -0.028 82 0.037 83
Bump severity 0.002 87 0.002 87
Hydrogen bond satisfaction 0.891 39 0.924 81
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 9
Side chains flipped 0
Waters removed 17
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 43
Residues fitting density worse 1
Change in density map fit (RSCC)