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Protruding domain of GII.4 human norovirus CHDC2094 in complex with HBGA type A (triglycan) |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | I 2 2 2 | a: 89.710 Å | b: 106.120 Å | c: 135.920 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 1.27 Å | Reflections | 175960 | Test set | 8798 (5.0%) | ||
R | 0.1349 | R-free | 0.1594 | ||||
According to PDB-REDO | |||||||
Resolution | 1.25 Å | Reflections | 175960 | Test set | 8798 (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 | |
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Crystallographic refinement | ||
R | 0.1480 | 0.1384 |
R-free | 0.1686 | 0.1607 |
Bond length RMS Z-score | 0.691 | 0.831 |
Bond angle RMS Z-score | 0.756 | 0.809 |
Model quality | ||
Ramachandran plot normality | -0.249 76 | -0.146 79 |
Rotamer normality | 1.196 98 | 0.982 98 |
Coarse packing | N/A N/A | N/A N/A |
Fine packing | N/A N/A | N/A N/A |
Bump severity | 0.000 95 | 0.000 95 |
Hydrogen bond satisfaction | N/A N/A | N/A N/A |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 12 |
Side chains flipped | 3 |
Waters removed | 44 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 51 |
Residues fitting density worse | 1 |