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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z54571979 |
| 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: 112.560 Å | b: 52.810 Å | c: 52.810 Å | α: 90.00° | β: 103.20° | γ: 90.00° |
| Resolution | 1.87 Å | Reflections | 21169 | Test set | 1077 (5.1%) | ||
| R | 0.1857 | R-free | 0.2505 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.87 Å | Reflections | 21169 | Test set | 1077 (5.1%) | ||
| Twin | false | Radiation damage | 17 | ||||
| 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 | 0.1955 | 0.2088 |
| R-free | 0.2564 | 0.2588 |
| Bond length RMS Z-score | 1.340 | 0.193 |
| Bond angle RMS Z-score | 1.020 | 0.440 |
| Model quality | ||
| Ramachandran plot normality | -1.514 42 | -1.087 53 |
| Rotamer normality | -1.849 54 | -0.432 83 |
| Coarse packing | 0.387 66 | 0.290 62 |
| Fine packing | -1.714 23 | -1.471 33 |
| Bump severity | 0.003 81 | 0.004 76 |
| Hydrogen bond satisfaction | 0.891 39 | 0.901 51 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 0 |
| Waters removed | 54 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |