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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z111507846 |
| 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: 113.973 Å | b: 52.913 Å | c: 52.913 Å | α: 90.00° | β: 103.02° | γ: 90.00° |
| Resolution | 1.80 Å | Reflections | 23299 | Test set | 1169 (5.0%) | ||
| R | 0.1871 | R-free | 0.2573 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.80 Å | Reflections | 23299 | Test set | 1169 (5.0%) | ||
| Twin | false | Radiation damage | 30 | ||||
| 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 | 0.1991 | 0.2137 |
| R-free | 0.2702 | 0.2660 |
| Bond length RMS Z-score | 1.364 | 0.191 |
| Bond angle RMS Z-score | 1.033 | 0.446 |
| Model quality | ||
| Ramachandran plot normality | -1.746 36 | -1.205 50 |
| Rotamer normality | -1.513 61 | -0.544 81 |
| Coarse packing | 0.347 64 | 0.363 65 |
| Fine packing | -1.630 26 | -1.312 40 |
| Bump severity | 0.028 29 | 0.007 65 |
| Hydrogen bond satisfaction | 0.891 39 | 0.896 45 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 5 |
| Side chains built | 0 |
| Waters removed | 79 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |