| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102395 |
| 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: 112.233 Å | b: 52.757 Å | c: 44.543 Å | α: 90.00° | β: 102.93° | γ: 90.00° |
| Resolution | 1.69 Å | Reflections | 28488 | Test set | 1410 (4.9%) | ||
| R | 0.1830 | R-free | 0.2323 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.69 Å | Reflections | 28488 | Test set | 1410 (4.9%) | ||
| Twin | false | Radiation damage | 14 | ||||
| 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 | 0.1903 | 0.1931 |
| R-free | 0.2359 | 0.2343 |
| Bond length RMS Z-score | 1.275 | 0.393 |
| Bond angle RMS Z-score | 0.985 | 0.603 |
| Model quality | ||
| Ramachandran plot normality | -1.182 50 | -0.960 56 |
| Rotamer normality | -0.907 74 | -0.311 85 |
| Coarse packing | 0.520 71 | 0.479 69 |
| Fine packing | -0.517 70 | -0.427 73 |
| Bump severity | 0.005 72 | 0.005 72 |
| Hydrogen bond satisfaction | 0.873 24 | 0.879 28 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 7 |
| Side chains flipped | 0 |
| Waters removed | 46 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |