This entry is not up to date with the most recent version of PDB-REDO.
Please log in
to request an update.
| 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: 112.812 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 | 0.1779 | 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 | 3D bionotes | 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 flipped | 0 |
| Waters removed | 62 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 199 |
| Residues fitting density worse | 0 |