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| SARS-CoV-2 main protease with unliganded active site (2019-nCoV, coronavirus disease 2019, COVID-19) |
| This entry was created with PDB-REDO version 8.08 using the deposited PDB model version 1.5 |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.812Å b: 52.949Å c: 44.631Å | α: 90.00° β: 103.16° γ: 90.00° | ||
| Resolution | 1.39 Å | Reflections | 50331 | Test set | 2585 (5.1%) |
| R | 0.1779 | R-free | 0.2000 | ||
| According to PDB-REDO | |||||
| Resolution | 1.39 Å | Reflections | 50331 | Test set | 2585 (5.1%) |
| Twin | false | Radiation damage | N/A | ||
| PDB-REDO files | |||||
| Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
|||
| Links | |||||
| PDBe | RCSB PDB | Proteopedia | |||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.1805 | 0.1362 |
| R-free |
0.2306
R-free was considered biased, the
estimated unbiased R-free was used
|
0.1727 |
| Bond length RMS Z-score | 0.744 | 0.945 |
| Bond angle RMS Z-score | 0.747 | 0.899 |
| Model quality | ||
| Ramachandran plot normality | -0.279 76 | -0.757 62 |
| Rotamer normality | 0.039 90 | 0.733 96 |
| Coarse packing | 0.350 64 | 0.443 68 |
| Fine packing | -1.711 23 | -1.584 28 |
| Bump severity | 0.001 90 | 0.004 76 |
| Hydrogen bond satisfaction | 0.890 38 | 0.891 39 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 4 |
| Side chains built | 0 |
| Waters removed | 62 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 199 |
| Residues fitting density worse | 0 |