| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102306 |
| This entry was created with PDB-REDO version 8.20 using the deposited PDB model version 1.6 |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.254Å b: 52.664Å c: 44.535Å | α: 90.00° β: 103.02° γ: 90.00° | ||
| Resolution | 1.48 Å | Reflections | 40622 | Test set | 1979 (4.9%) |
| R | 0.1873 | R-free | 0.2236 | ||
| According to PDB-REDO | |||||
| Resolution | 1.48 Å | Reflections | 40622 | Test set | 1979 (4.9%) |
| Twin | false | Radiation damage | 20 | ||
| PDB-REDO files | |||||
| Re-refined and rebuilt structure |
Re-refined (only) structure
|
All files
(compressed) |
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| Links | |||||
| PDBe | RCSB PDB | Proteopedia | |||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.1948 | 0.1979 |
| R-free | 0.2294 | 0.2267 |
| Bond length RMS Z-score | 1.284 | 0.346 |
| Bond angle RMS Z-score | 0.998 | 0.582 |
| Model quality | ||
| Ramachandran plot normality | -1.021 55 | -0.973 56 |
| Rotamer normality | -0.635 79 | 0.107 91 |
| Coarse packing | 0.523 71 | 0.466 69 |
| Fine packing | -0.524 70 | -0.462 72 |
| MolProbity Clashscore | 4.210 61 | 4.850 54 |
| Hydrogen bond satisfaction | 0.877 26 | 0.873 24 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | N/A |
| Side chains built | 0 |
| Waters removed | N/A |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |