| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102389 |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 1.5 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.043 Å | b: 52.569 Å | c: 44.672 Å | α: 90.00° | β: 103.02° | γ: 90.00° |
| Resolution | 1.64 Å | Reflections | 30829 | Test set | 1520 (4.9%) | ||
| R | 0.1843 | R-free | 0.2247 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.64 Å | Reflections | 30829 | Test set | 1520 (4.9%) | ||
| Twin | false | Radiation damage | 61 | ||||
| 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 | 0.2002 | 0.1961 |
| R-free | 0.2340 | 0.2303 |
| Bond length RMS Z-score | 1.271 | 0.364 |
| Bond angle RMS Z-score | 0.989 | 0.583 |
| Model quality | ||
| Ramachandran plot normality | -1.202 50 | -1.023 55 |
| Rotamer normality | -1.170 68 | -0.150 88 |
| Coarse packing | 0.472 69 | 0.421 67 |
| Fine packing | -0.548 70 | -0.427 73 |
| Bump severity | 0.004 76 | 0.006 68 |
| Hydrogen bond satisfaction | 0.871 22 | 0.866 20 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 6 |
| Side chains flipped | 0 |
| Waters removed | 39 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |