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Structure of the P domain from a GI.7 Norovirus variant in complex with LeY HBGA. |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | P 1 | a: 62.314 Å | b: 63.124 Å | c: 90.580 Å | α: 72.80° | β: 82.18° | γ: 60.85° |
Resolution | 1.50 Å | Reflections | 170683 | Test set | 8552 (5.0%) | ||
R | 0.1342 | R-free | 0.1745 | ||||
According to PDB-REDO | |||||||
Resolution | 1.50 Å | Reflections | 170683 | Test set | 8552 (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 | 0.1702 | 0.1473 |
R-free | 0.1955 R-free was considered biased, the estimated unbiased R-free was used | 0.1729 |
Bond length RMS Z-score | 0.728 | 0.765 |
Bond angle RMS Z-score | 0.870 | 0.909 |
Model quality | ||
Ramachandran plot normality | -0.159 79 | -0.149 79 |
Rotamer normality | 0.834 97 | 0.642 96 |
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 | 21 |
Side chains flipped | 3 |
Waters removed | 162 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 49 |
Residues fitting density worse | 0 |