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P domain of GII.13 norovirus capsid complexed with Lewis A trisaccharide |
This entry was created with PDB-REDO version 7.32. |
From original header | |||||||
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Spacegroup | P 21 21 21 | a: 67.230 Å | b: 82.618 Å | c: 116.142 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 1.80 Å | Reflections | 57460 | Test set | 2912 (5.1%) | ||
R | 0.1540 | R-free | 0.2010 | ||||
According to PDB-REDO | |||||||
Resolution | 1.80 Å | Reflections | 57460 | Test set | 2912 (5.1%) | ||
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 | 0.1546 | 0.1620 |
R-free | 0.2021 | 0.2008 |
Bond length RMS Z-score | 0.340 | 0.628 |
Bond angle RMS Z-score | 0.588 | 0.771 |
Model quality | ||
Ramachandran plot normality | -0.749 60 | -0.854 57 |
Rotamer normality | -0.408 87 | -0.686 83 |
Coarse packing | -1.028 15 | -1.023 15 |
Fine packing | -1.392 36 | -1.154 47 |
Bump severity | 0.069 14 | 0.063 15 |
Hydrogen bond satisfaction | 0.889 37 | 0.894 43 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 42 |
Side chains flipped | 0 |
Waters removed | 33 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 1 |
Residues fitting density worse | 0 |