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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102306 |
| This entry was created with PDB-REDO version 7.34. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.254 Å | b: 52.664 Å | c: 44.535 Å | α: 90.00° | β: 103.02° | γ: 90.00° |
| Resolution | 1.48 Å | Reflections | 40622 | Test set | 1979 (4.9%) | ||
| R | 0.1870 | R-free | 0.2240 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.48 Å | Reflections | 40622 | Test set | 1979 (4.9%) | ||
| Twin | false | Radiation damage | N/A | ||||
| 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 | 0.1950 | 0.1970 |
| R-free | 0.2298 | 0.2273 |
| Bond length RMS Z-score | 0.659 | 0.377 |
| Bond angle RMS Z-score | 1.020 | 0.667 |
| Model quality | ||
| Ramachandran plot normality | -1.083 51 | -0.977 54 |
| Rotamer normality | -0.636 83 | 0.085 93 |
| Coarse packing | -0.251 49 | -0.245 49 |
| Fine packing | -1.636 26 | -1.372 37 |
| Bump severity | 0.003 82 | 0.004 78 |
| Hydrogen bond satisfaction | 0.884 32 | 0.883 31 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 0 |
| Waters removed | 41 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |