| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102372 |
| 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: 113.335 Å | b: 53.266 Å | c: 44.411 Å | α: 90.00° | β: 103.18° | γ: 90.00° |
| Resolution | 2.32 Å | Reflections | 11232 | Test set | 576 (5.1%) | ||
| R | 0.2121 | R-free | 0.3065 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.32 Å | Reflections | 11232 | Test set | 576 (5.1%) | ||
| Twin | false | Radiation damage | 48 | ||||
| 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 | 0.2292 | 0.2253 |
| R-free | 0.3050 | 0.3070 |
| Bond length RMS Z-score | 1.316 | 0.161 |
| Bond angle RMS Z-score | 0.926 | 0.410 |
| Model quality | ||
| Ramachandran plot normality | -3.003 17 | -2.858 18 |
| Rotamer normality | -2.628 39 | -2.001 51 |
| Coarse packing | -0.044 47 | -0.087 45 |
| Fine packing | -0.832 60 | -0.973 54 |
| Bump severity | 0.008 62 | 0.009 59 |
| Hydrogen bond satisfaction | 0.833 10 | 0.833 10 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 7 |
| Side chains flipped | 0 |
| Waters removed | 64 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |