| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102287 |
| 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: 112.639 Å | b: 53.038 Å | c: 44.943 Å | α: 90.00° | β: 102.72° | γ: 90.00° |
| Resolution | 2.07 Å | Reflections | 15821 | Test set | 808 (5.1%) | ||
| R | 0.1749 | R-free | 0.2507 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.07 Å | Reflections | 15821 | Test set | 808 (5.1%) | ||
| Twin | false | Radiation damage | 49 | ||||
| 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 | 0.1859 | 0.2057 |
| R-free | 0.2580 | 0.2515 |
| Bond length RMS Z-score | 1.296 | 0.279 |
| Bond angle RMS Z-score | 0.968 | 0.491 |
| Model quality | ||
| Ramachandran plot normality | -1.982 31 | -1.278 48 |
| Rotamer normality | -2.305 45 | -1.335 65 |
| Coarse packing | 0.375 65 | 0.332 64 |
| Fine packing | -0.523 70 | -0.522 70 |
| Bump severity | 0.014 47 | 0.010 56 |
| Hydrogen bond satisfaction | 0.878 27 | 0.864 19 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 7 |
| Side chains flipped | 0 |
| Waters removed | 148 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 1 |
| Residues fitting density worse | 0 |