| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102254 |
| 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: 111.803 Å | b: 52.599 Å | c: 44.686 Å | α: 90.00° | β: 102.94° | γ: 90.00° |
| Resolution | 1.55 Å | Reflections | 36472 | Test set | 1793 (4.9%) | ||
| R | 0.1844 | R-free | 0.2163 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.55 Å | Reflections | 36472 | Test set | 1793 (4.9%) | ||
| Twin | false | Radiation damage | 23 | ||||
| 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 | 0.1923 | 0.1874 |
| R-free | 0.2229 | 0.2238 |
| Bond length RMS Z-score | 1.263 | 0.322 |
| Bond angle RMS Z-score | 0.961 | 0.569 |
| Model quality | ||
| Ramachandran plot normality | -1.132 52 | -1.007 55 |
| Rotamer normality | -0.886 74 | 0.077 91 |
| Coarse packing | 0.465 69 | 0.443 68 |
| Fine packing | -0.524 70 | -0.451 72 |
| Bump severity | 0.006 68 | 0.004 76 |
| Hydrogen bond satisfaction | 0.871 22 | 0.873 24 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 6 |
| Side chains flipped | 0 |
| Waters removed | 32 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 2 |
| Residues fitting density worse | 0 |