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| Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2. |
| This entry was created with PDB-REDO version 8.04 using the deposited PDB model version 2.2 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 63 | a: 150.539 Å | b: 150.539 Å | c: 111.310 Å | α: 90.00° | β: 90.00° | γ: 120.00° |
| Resolution | 2.20 Å | Reflections | 71192 | Test set | 3639 (5.1%) | ||
| R | 0.1577 | R-free | 0.1777 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.20 Å | Reflections | 71192 | Test set | 3639 (5.1%) | ||
| Twin | true | 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 | 0.1620 | 0.1430 |
| R-free | 0.1800 | 0.1616 |
| Bond length RMS Z-score | 0.590 | 0.966 |
| Bond angle RMS Z-score | 0.638 | 0.900 |
| Model quality | ||
| Ramachandran plot normality | -1.818 33 | -1.218 47 |
| Rotamer normality | -0.949 78 | -1.893 60 |
| Coarse packing | -0.214 51 | -0.244 49 |
| Fine packing | -1.693 24 | -1.541 30 |
| Bump severity | 0.011 56 | 0.005 74 |
| Hydrogen bond satisfaction | 0.899 49 | 0.920 77 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 7 |
| Side chains flipped | 2 |
| Waters removed | 16 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 18 |
| Residues fitting density worse | 1 |