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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z2643472210 |
| 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: 112.634 Å | b: 52.833 Å | c: 52.833 Å | α: 90.00° | β: 103.08° | γ: 90.00° |
| Resolution | 1.52 Å | Reflections | 38237 | Test set | 1856 (4.9%) | ||
| R | 0.1767 | R-free | 0.2151 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.52 Å | Reflections | 38237 | Test set | 1856 (4.9%) | ||
| Twin | false | Radiation damage | 23 | ||||
| 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 | 0.1854 | 0.1887 |
| R-free | 0.2225 | 0.2241 |
| Bond length RMS Z-score | 1.358 | 0.530 |
| Bond angle RMS Z-score | 0.999 | 0.665 |
| Model quality | ||
| Ramachandran plot normality | -0.849 60 | -0.759 62 |
| Rotamer normality | -0.784 76 | -0.249 86 |
| Coarse packing | 0.671 76 | 0.630 75 |
| Fine packing | -1.584 28 | -1.584 28 |
| Bump severity | 0.007 65 | 0.020 37 |
| Hydrogen bond satisfaction | 0.879 28 | 0.886 34 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 0 |
| Waters removed | 42 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |