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PDB-REDO Databank

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4drv redone
Cell attachment protein VP8* of a human rotavirus specifically interacts with A-type histo-blood group antigen

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

Crystallographic data
From PDB header
Spacegroup P 1 21 1 a: 43.720 Å b: 35.220 Å c: 43.990 Å α: 90.00° β: 95.45° γ: 90.00°
Resolution 1.56 Å Reflections 19352 Test set 989 (5.1%)
R 0.1500 R-free 0.1780
According to PDB-REDO
Resolution 1.56 Å Reflections 19352 Test set 989 (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 0.1436 0.1362
R-free 0.1717 0.1721
Bond length RMS Z-score 0.284 0.788
Bond angle RMS Z-score 0.465 0.824
Model quality (raw scores | percentiles)
Ramachandran plot appearance -1.846 33 -2.092 28
Rotamer normality 0.375 95 0.275 95
Coarse packing 0.276 75 0.239 73
Fine packing -1.854 18 -1.802 20
Bump severity 0.000 96 0.000 96
Hydrogen bond satisfaction 0.913 68 0.925 82
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 3
Side chains flipped 0
Waters removed 19
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 0
Residues fitting density worse 0
Change in density map fit (RSCC)