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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z979145504 |
| 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: 112.577 Å | b: 52.959 Å | c: 52.959 Å | α: 90.00° | β: 102.99° | γ: 90.00° |
| Resolution | 1.40 Å | Reflections | 46629 | Test set | 2260 (4.8%) | ||
| R | 0.1795 | R-free | 0.2128 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.40 Å | Reflections | 46629 | Test set | 2260 (4.8%) | ||
| Twin | false | Radiation damage | 14 | ||||
| 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 | 0.1851 | 0.1856 |
| R-free | 0.2177 | 0.2174 |
| Bond length RMS Z-score | 1.305 | 0.261 |
| Bond angle RMS Z-score | 1.017 | 0.535 |
| Model quality | ||
| Ramachandran plot normality | -0.323 75 | -0.337 74 |
| Rotamer normality | -0.303 85 | 0.518 95 |
| Coarse packing | 0.511 71 | 0.435 68 |
| Fine packing | -1.635 26 | -1.492 32 |
| Bump severity | 0.005 72 | 0.009 59 |
| Hydrogen bond satisfaction | 0.902 53 | 0.886 34 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 0 |
| Waters removed | 40 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 2 |
| Residues fitting density worse | 0 |