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Structure of the P domain from a GI.7 Norovirus variant in complex with A-type 2 HBGA |
This entry was created with PDB-REDO version 8.03. |
From original header | |||||||
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Spacegroup | P 1 | a: 62.580 Å | b: 63.260 Å | c: 90.430 Å | α: 99.25° | β: 97.82° | γ: 119.62° |
Resolution | 1.90 Å | Reflections | 87902 | Test set | 4403 (5.0%) | ||
R | 0.1597 | R-free | 0.1890 | ||||
According to PDB-REDO | |||||||
Resolution | 1.90 Å | Reflections | 87902 | Test set | 4403 (5.0%) | ||
Twin | false | Radiation damage | N/A | ||||
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 | |
---|---|---|
Crystallographic refinement | ||
R | 0.1659 | 0.1536 |
R-free | 0.1897 | 0.1861 |
Bond length RMS Z-score | 0.582 | 0.484 |
Bond angle RMS Z-score | 0.677 | 0.632 |
Model quality | ||
Ramachandran plot normality | -0.380 71 | -0.175 76 |
Rotamer normality | 0.411 96 | 0.195 94 |
Coarse packing | -1.220 11 | -1.238 10 |
Fine packing | -1.345 38 | -1.110 48 |
Bump severity | 0.022 37 | 0.013 51 |
Hydrogen bond satisfaction | 0.888 36 | 0.879 28 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 25 |
Side chains flipped | 8 |
Waters removed | 29 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 23 |
Residues fitting density worse | 0 |