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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z24758179 |
| 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: 112.514 Å | b: 52.708 Å | c: 52.708 Å | α: 90.00° | β: 103.04° | γ: 90.00° |
| Resolution | 1.61 Å | Reflections | 31983 | Test set | 1584 (5.0%) | ||
| R | 0.1981 | R-free | 0.2461 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.61 Å | Reflections | 31983 | Test set | 1584 (5.0%) | ||
| Twin | false | Radiation damage | 19 | ||||
| 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 | 0.2119 | 0.2082 |
| R-free | 0.2577 | 0.2565 |
| Bond length RMS Z-score | 1.349 | 0.445 |
| Bond angle RMS Z-score | 0.982 | 0.613 |
| Model quality | ||
| Ramachandran plot normality | -1.786 35 | -1.446 43 |
| Rotamer normality | -1.483 62 | -0.651 79 |
| Coarse packing | 0.416 67 | 0.288 62 |
| Fine packing | -1.592 28 | -1.527 30 |
| Bump severity | 0.004 76 | 0.009 59 |
| Hydrogen bond satisfaction | 0.887 35 | 0.896 45 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 7 |
| Side chains flipped | 0 |
| Waters removed | 63 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 1 |
| Residues fitting density worse | 0 |