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| crystal structure of the wildtype MHV coronavirus non-structural protein nsp15 |
| This entry was created with PDB-REDO version 7.00. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 63 2 2 | a: 86.435 Å | b: 86.435 Å | c: 219.220 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
| Resolution | 2.70 Å | Reflections | 9985 | Test set | 517 (5.2%) | ||
| R | 0.1950 | R-free | 0.2560 | ||||
| According to PDB-REDO | |||||||
| Resolution | 3.00 Å | Reflections | 9985 | Test set | 517 (5.2%) | Twin | false |
| 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 | 0.1970 | 0.2034 |
| R-free | 0.2644 | 0.2643 |
| Bond length RMS Z-score | 0.459 | 0.449 |
| Bond angle RMS Z-score | 0.699 | 0.650 |
| Model quality | ||
| Ramachandran plot normality | -3.287 10 | -1.515 31 |
| Rotamer normality | -4.200 9 | -3.058 21 |
| Coarse packing | -1.061 N/A | -0.891 N/A |
| Fine packing | -2.319 6 | -1.478 28 |
| Bump severity | 0.047 29 | 0.002 96 |
| Hydrogen bond satisfaction | 0.865 24 | 0.890 41 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 7 |
| Side chains flipped | 2 |
| Waters removed | 54 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 1 |
| Residues fitting density worse | 2 |