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Crystal structure of Norovirus Boxer P domain in complex with Lewis y tetrasaccharide |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | P 61 | a: 140.390 Å | b: 140.390 Å | c: 65.020 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
Resolution | 1.45 Å | Reflections | 129412 | Test set | 6496 (5.0%) | ||
R | 0.1304 | R-free | 0.1507 | ||||
According to PDB-REDO | |||||||
Resolution | 1.45 Å | Reflections | 129412 | Test set | 6496 (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 | 0.1247 | 0.1134 |
R-free | 0.1417 | 0.1363 |
Bond length RMS Z-score | 0.800 | 0.700 |
Bond angle RMS Z-score | 0.674 | 0.745 |
Model quality | ||
Ramachandran plot normality | -0.269 74 | -0.125 77 |
Rotamer normality | 0.671 97 | 0.580 96 |
Coarse packing | -0.993 16 | -1.041 15 |
Fine packing | -1.997 14 | -1.936 16 |
Bump severity | 0.001 92 | 0.017 44 |
Hydrogen bond satisfaction | 0.883 31 | 0.886 34 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 19 |
Side chains flipped | 0 |
Waters removed | 162 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 16 |
Residues fitting density worse | 2 |