Crystal structure of P domain from norovirus strain Saga4 in complex with HBGA type Leb (tetraglycan) |
This entry was created with PDB-REDO version 8.07. |
From original header | |||||||
---|---|---|---|---|---|---|---|
Spacegroup | C 1 2 1 | a: 113.660 Å | b: 58.600 Å | c: 58.600 Å | α: 90.00° | β: 107.15° | γ: 90.00° |
Resolution | 1.40 Å | Reflections | 124462 | Test set | 6224 (5.0%) | ||
R | 0.1508 | R-free | 0.1854 | ||||
According to PDB-REDO | |||||||
Resolution | 1.38 Å | Reflections | 124462 | Test set | 6224 (5.0%) | ||
Twin | false | Radiation damage | 67 | ||||
PDB-REDO files | |||||||
Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
|||||
Links | |||||||
PDBe | RCSB PDB | 3D bionotes | Proteopedia |
Original | PDB-REDO | |
---|---|---|
Crystallographic refinement | ||
R | 0.1570 | 0.1542 |
R-free | 0.1909 | 0.1844 |
Bond length RMS Z-score | 0.652 | 0.787 |
Bond angle RMS Z-score | 0.746 | 0.807 |
Model quality | ||
Ramachandran plot normality | -0.462 71 | -0.590 67 |
Rotamer normality | 0.930 97 | 0.867 97 |
Coarse packing | -0.912 14 | -0.963 12 |
Fine packing | -1.353 38 | -1.282 41 |
Bump severity | 0.098 10 | 0.099 10 |
Hydrogen bond satisfaction | 0.881 29 | 0.894 42 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 11 |
Side chains flipped | 6 |
Waters removed | 100 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 12 |
Residues fitting density worse | 0 |