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PDB-REDO Databank

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3pa2 redone
Crystal Structure of P Domain from Norwalk Virus Strain Vietnam 026 in complex with HBGA type Ley

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

Crystallographic data
From PDB header
Spacegroup P 1 21 1 a: 65.271 Å b: 79.130 Å c: 69.069 Å α: 90.00° β: 100.27° γ: 90.00°
Resolution 1.48 Å Reflections 114584 Test set 5767 (5.0%)
R 0.1850 R-free 0.2040
According to PDB-REDO
Resolution 1.48 Å Reflections 114584 Test set 5767 (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 0.1778 0.1492
R-free 0.1972 0.1874
Bond length RMS Z-score 0.343 0.632
Bond angle RMS Z-score 0.550 0.758
Model quality (raw scores | percentiles)
Ramachandran plot appearance -0.573 65 -0.303 73
Rotamer normality 1.103 98 0.842 98
Coarse packing -1.186 11 -1.224 11
Fine packing -1.705 23 -1.591 28
Bump severity 0.051 19 0.047 20
Hydrogen bond satisfaction 0.876 25 0.891 39
WHAT_CHECK Report Report

Kleywegt-like plot

Model quality compared to resolution neighbours
Significant model changes
Description Count
Rotamers changed 10
Side chains flipped 5
Waters removed 80
Peptides flipped 0
Chiralities fixed 0
Residues fitting density better 48
Residues fitting density worse 0
Change in density map fit (RSCC)