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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z2856434899 |
| 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: 113.212 Å | b: 53.034 Å | c: 53.034 Å | α: 90.00° | β: 102.95° | γ: 90.00° |
| Resolution | 1.68 Å | Reflections | 29081 | Test set | 1434 (4.9%) | ||
| R | 0.1755 | R-free | 0.2237 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.68 Å | Reflections | 29081 | Test set | 1434 (4.9%) | ||
| Twin | false | Radiation damage | 10 | ||||
| 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 | 0.1836 | 0.1856 |
| R-free | 0.2283 | 0.2258 |
| Bond length RMS Z-score | 1.420 | 0.619 |
| Bond angle RMS Z-score | 0.998 | 0.740 |
| Model quality | ||
| Ramachandran plot normality | -1.115 52 | -1.022 55 |
| Rotamer normality | -1.200 68 | -0.396 84 |
| Coarse packing | 0.470 69 | 0.414 67 |
| Fine packing | -1.562 29 | -1.337 39 |
| Bump severity | 0.008 62 | 0.008 62 |
| Hydrogen bond satisfaction | 0.879 28 | 0.886 34 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 11 |
| Side chains flipped | 0 |
| Waters removed | 77 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 2 |
| Residues fitting density worse | 0 |