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| PanDDA analysis group deposition -- Crystal Structure of COVID-19 main protease in complex with Z45617795 |
| 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: 112.463 Å | b: 52.731 Å | c: 52.731 Å | α: 90.00° | β: 102.81° | γ: 90.00° |
| Resolution | 1.65 Å | Reflections | 30223 | Test set | 1501 (5.0%) | ||
| R | 0.1794 | R-free | 0.2367 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.65 Å | Reflections | 30223 | Test set | 1501 (5.0%) | ||
| Twin | false | Radiation damage | 15 | ||||
| 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 | 0.2350 | 0.1985 |
| R-free | 0.2614 | 0.2450 |
| Bond length RMS Z-score | 1.374 | 0.389 |
| Bond angle RMS Z-score | 1.014 | 0.588 |
| Model quality | ||
| Ramachandran plot normality | -1.690 37 | -0.881 59 |
| Rotamer normality | -1.675 57 | -0.309 85 |
| Coarse packing | 0.425 67 | 0.477 69 |
| Fine packing | -1.554 29 | -1.465 33 |
| Bump severity | 0.009 59 | 0.017 42 |
| 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 | 92 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 70 |
| Residues fitting density worse | 0 |