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Crystal structure of Norovirus Boxer P domain in complex with Lewis b tetrasaccharide |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | P 61 | a: 139.866 Å | b: 139.866 Å | c: 64.789 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
Resolution | 1.63 Å | Reflections | 90234 | Test set | 4527 (5.0%) | ||
R | 0.1312 | R-free | 0.1665 | ||||
According to PDB-REDO | |||||||
Resolution | 1.63 Å | Reflections | 90234 | Test set | 4527 (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 | 0.1304 | 0.1485 |
R-free | 0.1606 | 0.1670 |
Bond length RMS Z-score | 0.718 | 0.613 |
Bond angle RMS Z-score | 0.662 | 0.706 |
Model quality | ||
Ramachandran plot normality | -0.144 77 | 0.105 82 |
Rotamer normality | 0.583 96 | 0.427 96 |
Coarse packing | -1.046 15 | -1.086 14 |
Fine packing | -1.816 20 | -1.843 19 |
Bump severity | 0.002 87 | 0.001 92 |
Hydrogen bond satisfaction | 0.880 28 | 0.895 44 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 12 |
Side chains flipped | 0 |
Waters removed | 8 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 1 |