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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 8.17 using the deposited PDB model version 3.3 |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.429Å b: 52.798Å c: 44.611Å | α: 90.00° β: 103.03° γ: 90.00° | ||
| Resolution | 1.25 Å | Reflections | 68358 | Test set | 3501 (5.1%) |
| R | 0.1417 | R-free | 0.1803 | ||
| According to PDB-REDO | |||||
| Resolution | 1.25 Å | Reflections | 68358 | Test set | 3501 (5.1%) |
| Twin | false | Radiation damage | 13 | ||
| 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 | 0.1432 | 0.1622 |
| R-free |
0.1769
R-free was considered biased, the
estimated unbiased R-free was used
|
0.1822 |
| Bond length RMS Z-score | 1.184 | 0.456 |
| Bond angle RMS Z-score | 0.893 | 0.676 |
| Model quality | ||
| Ramachandran plot normality | -0.221 77 | -0.479 70 |
| Rotamer normality | 0.706 96 | 0.612 95 |
| Coarse packing | 0.490 70 | 0.451 68 |
| Fine packing | -0.191 79 | -0.325 76 |
| MolProbity Clashscore | 2.540 81 | 3.120 74 |
| Hydrogen bond satisfaction | 0.871 22 | 0.878 27 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 4 |
| Side chains built | 0 |
| Waters removed | 84 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 6 |