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Structure of the P domain from a GI.7 Norovirus variant in complex with LeA HBGA. |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | P 1 | a: 62.168 Å | b: 63.277 Å | c: 90.400 Å | α: 72.77° | β: 82.20° | γ: 60.31° |
Resolution | 1.69 Å | Reflections | 122274 | Test set | 6146 (5.0%) | ||
R | 0.1551 | R-free | 0.1774 | ||||
According to PDB-REDO | |||||||
Resolution | 1.69 Å | Reflections | 122274 | Test set | 6146 (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 | 0.1611 | 0.1482 |
R-free | 0.1782 | 0.1746 |
Bond length RMS Z-score | 0.826 | 0.714 |
Bond angle RMS Z-score | 0.925 | 0.853 |
Model quality | ||
Ramachandran plot normality | -0.336 74 | -0.054 81 |
Rotamer normality | 0.974 97 | 0.395 94 |
Coarse packing | N/A N/A | N/A N/A |
Fine packing | N/A N/A | N/A N/A |
Bump severity | 0.000 95 | 0.000 95 |
Hydrogen bond satisfaction | N/A N/A | N/A N/A |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 25 |
Side chains flipped | 12 |
Waters removed | 137 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 17 |
Residues fitting density worse | 0 |