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4d71 redone
Crystal structure of a family 98 glycoside hydrolase catalytic module (Sp3GH98) in complex with the type 2 blood group A-tetrasaccharide (E558A X02 mutant)

This information was created with PDB-REDO version 7.31. Please log in to request an update.

Crystallographic data
From PDB header
Spacegroup C 2 2 21 a: 92.330 Å b: 155.020 Å c: 97.260 Å α: 90.00° β: 90.00° γ: 90.00°
Resolution 1.77 Å Reflections 67320 Test set 3399 (5.0%)
R 0.1630 R-free 0.2010
According to PDB-REDO
Resolution 1.77 Å Reflections 67320 Test set 3399 (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 0.1562 0.1465
R-free 0.1914 0.1854
Bond length RMS Z-score 0.502 0.634
Bond angle RMS Z-score 0.633 0.781
Model quality (raw scores | percentiles)
Ramachandran plot appearance -0.923 55 -0.986 54
Rotamer normality -0.370 88 -0.114 91
Coarse packing -0.119 56 -0.101 56
Fine packing -2.200 10 -2.087 12
Bump severity 0.001 92 0.001 92
Hydrogen bond satisfaction 0.885 33 0.885 33
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 22
Side chains flipped 6
Waters removed 32
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 0
Residues fitting density worse 0
Change in density map fit (RSCC)