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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1741970824 |
| 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: 112.469 Å | b: 52.697 Å | c: 52.697 Å | α: 90.00° | β: 103.06° | γ: 90.00° |
| Resolution | 1.50 Å | Reflections | 40023 | Test set | 1943 (4.9%) | ||
| R | 0.1853 | R-free | 0.2210 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.50 Å | Reflections | 40023 | Test set | 1943 (4.9%) | ||
| Twin | false | Radiation damage | 5 | ||||
| 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 | 0.2044 | 0.2030 |
| R-free | 0.2402 | 0.2412 |
| Bond length RMS Z-score | 1.274 | 0.342 |
| Bond angle RMS Z-score | 0.969 | 0.572 |
| Model quality | ||
| Ramachandran plot normality | -0.850 60 | -0.686 64 |
| Rotamer normality | -0.685 78 | 0.019 90 |
| Coarse packing | 0.561 72 | 0.481 69 |
| Fine packing | -1.579 28 | -1.461 33 |
| Bump severity | 0.002 85 | 0.003 81 |
| Hydrogen bond satisfaction | 0.872 23 | 0.887 35 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 6 |
| Side chains flipped | 0 |
| Waters removed | 30 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |