| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102425 |
| 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: 113.544 Å | b: 52.903 Å | c: 44.618 Å | α: 90.00° | β: 103.16° | γ: 90.00° |
| Resolution | 2.15 Å | Reflections | 14085 | Test set | 725 (5.1%) | ||
| R | 0.1738 | R-free | 0.2779 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.15 Å | Reflections | 14085 | Test set | 725 (5.1%) | ||
| Twin | false | Radiation damage | 7 | ||||
| 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 | 0.1875 | 0.2000 |
| R-free | 0.2870 | 0.2812 |
| Bond length RMS Z-score | 1.353 | 0.186 |
| Bond angle RMS Z-score | 1.008 | 0.427 |
| Model quality | ||
| Ramachandran plot normality | -2.798 19 | -1.955 32 |
| Rotamer normality | -2.638 38 | -0.518 82 |
| Coarse packing | 0.063 52 | -0.058 46 |
| Fine packing | -0.903 57 | -0.786 62 |
| Bump severity | 0.006 68 | 0.001 90 |
| Hydrogen bond satisfaction | 0.855 15 | 0.847 13 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 0 |
| Waters removed | 78 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |