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| PanDDA analysis group deposition -- Crystal Structure of COVID-19 main protease in complex with Z31792168 |
| 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: 113.146 Å | b: 53.167 Å | c: 53.167 Å | α: 90.00° | β: 101.66° | γ: 90.00° |
| Resolution | 1.83 Å | Reflections | 22784 | Test set | 1152 (5.1%) | ||
| R | 0.2167 | R-free | 0.2926 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.83 Å | Reflections | 22784 | Test set | 1152 (5.1%) | ||
| Twin | false | Radiation damage | 4 | ||||
| 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 | 0.2546 | 0.2563 |
| R-free | 0.2947 | 0.3048 |
| Bond length RMS Z-score | 1.368 | 0.260 |
| Bond angle RMS Z-score | 0.981 | 0.500 |
| Model quality | ||
| Ramachandran plot normality | -3.027 17 | -2.267 26 |
| Rotamer normality | -2.434 42 | -1.681 57 |
| Coarse packing | 0.303 63 | 0.274 61 |
| Fine packing | -1.672 25 | -1.510 31 |
| Bump severity | 0.047 19 | 0.056 16 |
| Hydrogen bond satisfaction | 0.891 39 | 0.887 35 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 0 |
| Waters removed | 83 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |