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PDB-REDO Databank

The PDB-REDO databank contains optimised versions of existing PDB entries with electron density maps, a description of model changes, and a wealth of model validation data. It is a good starting point for any structural biology project.

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4ds0 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: 43.750 Å b: 35.540 Å c: 44.060 Å α: 90.00° β: 94.85° γ: 90.00°
Resolution 1.56 Å Reflections 18212 Test set 939 (5.2%)
R 0.1560 R-free 0.1870
According to PDB-REDO
Resolution 1.56 Å Reflections 18212 Test set 939 (5.2%) 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 0.1481 0.1491
R-free 0.1764 0.1764
Bond length RMS Z-score 0.321 0.560
Bond angle RMS Z-score 0.491 0.725
Model quality (raw scores | percentiles)
Ramachandran plot appearance -1.849 32 -1.841 33
Rotamer normality -0.285 89 -0.567 85
Coarse packing 0.293 75 0.282 75
Fine packing -1.629 26 -1.681 24
Bump severity 0.000 96 0.000 96
Hydrogen bond satisfaction 0.918 75 0.920 77
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 5
Side chains flipped 0
Waters removed 23
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 0
Residues fitting density worse 0
Change in density map fit (RSCC)