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Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1 in complex with sialylated precision glycooligomers |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | P 21 21 21 | a: 139.277 Å | b: 146.160 Å | c: 150.413 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 1.98 Å | Reflections | 212141 | Test set | 2122 (1.0%) | ||
R | 0.1847 | R-free | 0.2299 | ||||
According to PDB-REDO | |||||||
Resolution | 1.98 Å | Reflections | 212141 | Test set | 2122 (1.0%) | ||
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 | 0.1854 | 0.1874 |
R-free | 0.2306 | 0.2251 |
Bond length RMS Z-score | 0.822 | 0.428 |
Bond angle RMS Z-score | 0.778 | 0.600 |
Model quality | ||
Ramachandran plot normality | 0.827 94 | 0.886 94 |
Rotamer normality | -0.114 88 | 0.205 92 |
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 | 67 |
Side chains flipped | 112 |
Waters removed | 72 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 3 |
Residues fitting density worse | 0 |