| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102243 |
| 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: 112.828Å b: 53.056Å c: 44.493Å | α: 90.00° β: 103.19° γ: 90.00° | ||
| Resolution | 1.43 Å | Reflections | 46157 | Test set | 2235 (4.8%) |
| R | 0.1895 | R-free | 0.2232 | ||
| According to PDB-REDO | |||||
| Resolution | 1.43 Å | Reflections | 46157 | Test set | 2235 (4.8%) |
| Twin | false | Radiation damage | 6 | ||
| 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 | 0.2059 | 0.1967 |
| R-free | 0.2397 | 0.2343 |
| Bond length RMS Z-score | 1.277 | 0.964 |
| Bond angle RMS Z-score | 1.047 | 0.966 |
| Model quality | ||
| Ramachandran plot normality | -0.592 67 | -0.734 63 |
| Rotamer normality | -0.900 74 | -0.542 81 |
| Coarse packing | 0.462 69 | 0.414 67 |
| Fine packing | -0.512 71 | -0.460 72 |
| MolProbity Clashscore | 5.460 49 | 6.940 38 |
| Hydrogen bond satisfaction | 0.860 17 | 0.868 21 |
| 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 | 3 |
| Residues fitting density worse | 0 |