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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z217038356 |
| 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: 111.967 Å | b: 52.499 Å | c: 52.499 Å | α: 90.00° | β: 102.92° | γ: 90.00° |
| Resolution | 1.43 Å | Reflections | 44145 | Test set | 2146 (4.9%) | ||
| R | 0.1820 | R-free | 0.2154 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.43 Å | Reflections | 44145 | Test set | 2146 (4.9%) | ||
| Twin | false | Radiation damage | 24 | ||||
| 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 | 0.1937 | 0.1905 |
| R-free | 0.2301 | 0.2319 |
| Bond length RMS Z-score | 1.282 | 0.468 |
| Bond angle RMS Z-score | 1.003 | 0.645 |
| Model quality | ||
| Ramachandran plot normality | -0.847 60 | -0.675 65 |
| Rotamer normality | -0.902 74 | -0.140 88 |
| Coarse packing | 0.507 70 | 0.486 70 |
| Fine packing | -1.546 30 | -1.484 32 |
| Bump severity | 0.006 68 | 0.012 51 |
| Hydrogen bond satisfaction | 0.906 58 | 0.907 59 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 0 |
| Waters removed | 49 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 1 |
| Residues fitting density worse | 0 |