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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1587220559 |
| 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: 112.398 Å | b: 52.720 Å | c: 52.720 Å | α: 90.00° | β: 102.89° | γ: 90.00° |
| Resolution | 1.73 Å | Reflections | 26435 | Test set | 1314 (5.0%) | ||
| R | 0.1826 | R-free | 0.2371 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.73 Å | Reflections | 26435 | Test set | 1314 (5.0%) | ||
| Twin | false | Radiation damage | 22 | ||||
| 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 | 0.1938 | 0.1999 |
| R-free | 0.2485 | 0.2415 |
| Bond length RMS Z-score | 1.324 | 0.322 |
| Bond angle RMS Z-score | 0.982 | 0.533 |
| Model quality | ||
| Ramachandran plot normality | -1.684 38 | -1.273 48 |
| Rotamer normality | -1.472 62 | -0.674 79 |
| Coarse packing | 0.461 69 | 0.413 67 |
| Fine packing | -1.608 27 | -1.365 37 |
| Bump severity | 0.006 68 | 0.006 68 |
| Hydrogen bond satisfaction | 0.894 42 | 0.888 36 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 9 |
| Side chains flipped | 0 |
| Waters removed | 84 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |