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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 8.01. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.812 Å | b: 52.949 Å | c: 44.631 Å | α: 90.00° | β: 103.16° | γ: 90.00° |
| Resolution | 1.39 Å | Reflections | 50331 | Test set | 2585 (5.1%) | ||
| R | 0.1780 | R-free | 0.2000 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.39 Å | Reflections | 50331 | Test set | 2585 (5.1%) | Twin | false |
| PDB-REDO files | |||||||
| Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
|||||
| Links | |||||||
| PDBe | RCSB PDB | 3D bionotes | Proteopedia | ||||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.1801 | 0.1855 |
| R-free |
0.2067
R-free was considered biased, the
estimated unbiased R-free was used
|
0.2005 |
| Bond length RMS Z-score | 0.457 | 0.507 |
| Bond angle RMS Z-score | 0.777 | 0.839 |
| Model quality | ||
| Ramachandran plot normality | -0.277 74 | -0.828 58 |
| Rotamer normality | 0.040 93 | 0.728 97 |
| Coarse packing | 0.350 78 | 0.422 80 |
| Fine packing | -1.712 23 | -1.616 27 |
| Bump severity | 0.001 92 | 0.005 74 |
| Hydrogen bond satisfaction | 0.891 39 | 0.896 45 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 2 |
| Side chains flipped | 0 |
| Waters removed | 53 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 9 |
| Residues fitting density worse | 0 |