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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z2217052426 |
| This entry was created with PDB-REDO version 8.07 using the deposited PDB model version 1.5 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 113.058 Å | b: 52.901 Å | c: 52.901 Å | α: 90.00° | β: 102.73° | γ: 90.00° |
| Resolution | 1.77 Å | Reflections | 24643 | Test set | 1232 (5.0%) | ||
| R | 0.1832 | R-free | 0.2424 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.77 Å | Reflections | 24643 | Test set | 1232 (5.0%) | ||
| Twin | false | Radiation damage | 32 | ||||
| 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 | 0.1975 |
| R-free | 0.2477 | 0.2473 |
| Bond length RMS Z-score | 1.387 | 0.481 |
| Bond angle RMS Z-score | 0.988 | 0.643 |
| Model quality | ||
| Ramachandran plot normality | -1.512 42 | -1.200 50 |
| Rotamer normality | -1.163 69 | -1.215 68 |
| Coarse packing | 0.480 69 | 0.433 68 |
| Fine packing | -1.500 32 | -1.340 39 |
| Bump severity | 0.008 62 | 0.019 39 |
| Hydrogen bond satisfaction | 0.895 43 | 0.888 36 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 0 |
| Waters removed | 84 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |