Crystal structure of P domain from Norovirus Funabashi258 stain in the complex with A-antigen |
This entry was created with PDB-REDO version 8.07. |
From original header | |||||||
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Spacegroup | P 31 | a: 74.624 Å | b: 74.624 Å | c: 74.624 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
Resolution | 1.60 Å | Reflections | 87885 | Test set | 4406 (5.0%) | ||
R | 0.1824 | R-free | 0.2007 | ||||
According to PDB-REDO | |||||||
Resolution | 1.60 Å | Reflections | 87885 | Test set | 4406 (5.0%) | ||
Twin | false | Radiation damage | 57 | ||||
PDB-REDO files | |||||||
Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
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Links | |||||||
PDBe | RCSB PDB | 3D bionotes | Proteopedia |
Original | PDB-REDO | |
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Crystallographic refinement | ||
R | 0.1737 | 0.1428 |
R-free | 0.1894 | 0.1651 |
Bond length RMS Z-score | 0.609 | 0.784 |
Bond angle RMS Z-score | 0.635 | 0.799 |
Model quality | ||
Ramachandran plot normality | -0.023 82 | 0.146 85 |
Rotamer normality | -0.110 88 | -0.058 89 |
Coarse packing | -1.220 8 | -1.265 7 |
Fine packing | -0.402 74 | -0.295 77 |
Bump severity | 0.001 90 | 0.004 76 |
Hydrogen bond satisfaction | 0.886 34 | 0.888 36 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 16 |
Side chains flipped | 0 |
Waters removed | 5 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 39 |
Residues fitting density worse | 0 |