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Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1 in complex with GM1 oligosaccharide |
This entry was created with PDB-REDO version 8.04. |
From original header | |||||||
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Spacegroup | P 21 21 2 | a: 144.990 Å | b: 152.050 Å | c: 67.970 Å | α: 90.00° | β: 90.00° | γ: 90.00° |
Resolution | 1.50 Å | Reflections | 238441 | Test set | 11948 (5.0%) | ||
R | 0.1576 | R-free | 0.1799 | ||||
According to PDB-REDO | |||||||
Resolution | 1.50 Å | Reflections | 238441 | Test set | 11948 (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 | 0.1576 | 0.1512 |
R-free | 0.1802 | 0.1732 |
Bond length RMS Z-score | 0.988 | 0.585 |
Bond angle RMS Z-score | 0.935 | 0.808 |
Model quality | ||
Ramachandran plot normality | 0.677 92 | 0.915 94 |
Rotamer normality | 0.513 95 | 0.724 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 | 43 |
Side chains flipped | 18 |
Waters removed | 42 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 26 |
Residues fitting density worse | 0 |