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3wg1 redone
Crystal structure of Agrocybe cylindracea galectin with lactose

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

Crystallographic data
From PDB header
Spacegroup P 61 a: 125.368 Å b: 125.368 Å c: 56.589 Å α: 90.00° β: 90.00° γ: 120.00°
Resolution 1.90 Å Reflections 39725 Test set 2034 (5.1%)
R 0.1730 R-free 0.1960
According to PDB-REDO
Resolution 1.90 Å Reflections 39725 Test set 2034 (5.1%) Twin false
PDB-REDO files
Re-refined and rebuilt structure
( PDB | mmCIF | MTZ)
Re-refined (only) structure
( PDB | MTZ)
All files
(compressed)
Links
PDBe RCSB PDB 3D bionotes Proteopedia
Validation metrics from PDB-REDO
PDB PDB-REDO
Crystallographic refinement
R 0.1778 0.1701
R-free 0.1937 0.1902
Bond length RMS Z-score 0.713 0.641
Bond angle RMS Z-score 0.863 0.860
Model quality (raw scores | percentiles)
Ramachandran plot appearance -2.210 26 -1.355 44
Rotamer normality -3.278 36 -2.385 51
Coarse packing 1.975 99 2.033 99
Fine packing 0.233 86 0.373 88
Bump severity 0.014 49 0.014 49
Hydrogen bond satisfaction 0.906 58 0.919 76
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 7
Side chains flipped 0
Waters removed 1
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 1
Residues fitting density worse 0
Change in density map fit (RSCC)