| The crystal structure of COVID-19 main protease in complex with an inhibitor N3 |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 4.2 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 97.931 Å | b: 79.477 Å | c: 51.803 Å | α: 90.00° | β: 114.55° | γ: 90.00° |
| Resolution | 2.16 Å | Reflections | 19454 | Test set | 998 (5.1%) | ||
| R | 0.2020 | R-free | 0.2350 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.16 Å | Reflections | 19454 | Test set | 998 (5.1%) | ||
| Twin | false | Radiation damage |
98
Data shows severe radiation damage
|
||||
| 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 | 0.2200 | 0.1789 |
| R-free | 0.2513 | 0.2190 |
| Bond length RMS Z-score | 0.797 | 0.343 |
| Bond angle RMS Z-score | 0.890 | 0.569 |
| Model quality | ||
| Ramachandran plot normality | -1.928 32 | -1.616 39 |
| Rotamer normality | -2.684 38 | -0.712 78 |
| Coarse packing | -0.023 48 | 0.182 57 |
| Fine packing | -0.706 64 | -0.551 69 |
| Bump severity | 0.012 51 | 0.013 49 |
| Hydrogen bond satisfaction | 0.849 13 | 0.866 20 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 5 |
| Side chains flipped | 0 |
| Waters removed | 11 |
| Peptides flipped | 1 |
| Chiralities fixed | 0 |
| Residues fitting density better | 19 |
| Residues fitting density worse | 0 |