Crystal structure of P domain from norovirus strain Farmington Hills 2004 in complex with HBGA type Leb (tetraglycan) |
This entry was created with PDB-REDO version 8.07. |
From original header | |||||||
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Spacegroup | P 21 21 21 | a: 71.450 Å | b: 90.110 Å | c: 90.110 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 1.76 Å | Reflections | 59028 | Test set | 2952 (5.0%) | ||
R | 0.1850 | R-free | 0.2164 | ||||
According to PDB-REDO | |||||||
Resolution | 1.75 Å | Reflections | 59028 | Test set | 2952 (5.0%) | ||
Twin | false | Radiation damage | 100 Data shows severe radiation damage | ||||
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 | |
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Crystallographic refinement | ||
R | 0.2009 | 0.2013 |
R-free | 0.2288 | 0.2206 |
Bond length RMS Z-score | 0.914 | 0.513 |
Bond angle RMS Z-score | 0.826 | 0.652 |
Model quality | ||
Ramachandran plot normality | 0.223 86 | -0.075 80 |
Rotamer normality | -0.227 86 | 0.266 93 |
Coarse packing | -1.082 10 | -1.054 10 |
Fine packing | -0.896 57 | -0.861 59 |
Bump severity | 0.057 16 | 0.053 17 |
Hydrogen bond satisfaction | 0.897 46 | 0.897 46 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 11 |
Side chains flipped | 8 |
Waters removed | 6 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 2 |
Residues fitting density worse | 0 |