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| The crystal structure of COVID-19 main protease in apo form |
| This entry was created with PDB-REDO version 8.04 using the deposited PDB model version 1.5 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 113.964 Å | b: 53.450 Å | c: 45.029 Å | α: 90.00° | β: 101.83° | γ: 90.00° |
| Resolution | 2.00 Å | Reflections | 18287 | Test set | 1827 (10%) | ||
| R | 0.1962 | R-free | 0.2458 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.99 Å | Reflections | 18287 | Test set | 1827 (10%) | ||
| 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 | 0.2102 | 0.1961 |
| R-free | 0.2560 | 0.2453 |
| Bond length RMS Z-score | 0.456 | 0.420 |
| Bond angle RMS Z-score | 0.670 | 0.626 |
| Model quality | ||
| Ramachandran plot normality | -0.860 57 | -1.497 40 |
| Rotamer normality | -2.518 48 | -1.514 68 |
| Coarse packing | 0.212 72 | 0.162 70 |
| Fine packing | -1.252 42 | -0.796 61 |
| Bump severity | 0.009 61 | 0.012 53 |
| Hydrogen bond satisfaction | 0.637 1 | 0.912 67 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 7 |
| Side chains flipped | 0 |
| Waters removed | 21 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 1 |
| Residues fitting density worse | 0 |