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| PanDDA analysis group deposition -- Crystal Structure of COVID-19 main protease in complex with Z1367324110 |
| 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: 113.780 Å | b: 53.490 Å | c: 53.490 Å | α: 90.00° | β: 101.70° | γ: 90.00° |
| Resolution | 1.95 Å | Reflections | 19192 | Test set | 985 (5.1%) | ||
| R | 0.1820 | R-free | 0.2494 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.95 Å | Reflections | 19192 | Test set | 985 (5.1%) | ||
| Twin | false | Radiation damage | 39 | ||||
| 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 | 0.2078 | 0.2080 |
| R-free | 0.2457 | 0.2499 |
| Bond length RMS Z-score | 1.348 | 0.207 |
| Bond angle RMS Z-score | 1.021 | 0.457 |
| Model quality | ||
| Ramachandran plot normality | -2.251 27 | -1.497 42 |
| Rotamer normality | -2.713 37 | -1.266 66 |
| Coarse packing | 0.334 64 | 0.300 62 |
| Fine packing | -1.623 27 | -1.378 37 |
| Bump severity | 0.009 59 | 0.004 76 |
| Hydrogen bond satisfaction | 0.852 14 | 0.891 39 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 7 |
| Side chains flipped | 0 |
| Waters removed | 132 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 1 |
| Residues fitting density worse | 0 |