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| Crystal Structure of ADP ribose phosphatase of NSP3 from SARS CoV-2 |
| This entry was created with PDB-REDO version 8.04. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | P 1 | a: 30.391 Å | b: 37.896 Å | c: 65.400 Å | α: 84.37° | β: 82.11° | γ: 90.11° |
| Resolution | 2.03 Å | Reflections | 15783 | Test set | 770 (4.9%) | ||
| R | 0.1864 | R-free | 0.2335 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.03 Å | Reflections | 15783 | Test set | 770 (4.9%) | ||
| 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 | 0.1996 | 0.1697 |
| R-free | 0.2350 | 0.2280 |
| Bond length RMS Z-score | 0.463 | 0.254 |
| Bond angle RMS Z-score | 0.663 | 0.476 |
| Model quality | ||
| Ramachandran plot normality | -0.789 59 | -0.367 71 |
| Rotamer normality | -1.562 67 | -0.588 84 |
| Coarse packing | 1.464 98 | 1.593 98 |
| Fine packing | -1.220 44 | -0.989 53 |
| Bump severity | 0.004 78 | 0.005 74 |
| Hydrogen bond satisfaction | 0.915 71 | 0.917 73 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 9 |
| Side chains flipped | 0 |
| Waters removed | 12 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 7 |
| Residues fitting density worse | 0 |