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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with NCL-00023830 |
| 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: 112.485 Å | b: 52.653 Å | c: 52.653 Å | α: 90.00° | β: 102.74° | γ: 90.00° |
| Resolution | 1.73 Å | Reflections | 26410 | Test set | 1314 (5.0%) | ||
| R | 0.1862 | R-free | 0.2361 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.73 Å | Reflections | 26410 | Test set | 1314 (5.0%) | ||
| Twin | false | Radiation damage | 6 | ||||
| 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 | 0.1993 | 0.2069 |
| R-free | 0.2462 | 0.2454 |
| Bond length RMS Z-score | 1.326 | 0.186 |
| Bond angle RMS Z-score | 0.974 | 0.441 |
| Model quality | ||
| Ramachandran plot normality | -2.130 29 | -1.085 53 |
| Rotamer normality | -1.422 63 | -0.166 87 |
| Coarse packing | 0.481 69 | 0.375 65 |
| Fine packing | -1.618 27 | -1.345 38 |
| Bump severity | 0.005 72 | 0.003 81 |
| Hydrogen bond satisfaction | 0.887 35 | 0.888 36 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 6 |
| Side chains flipped | 0 |
| Waters removed | 68 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |