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| PanDDA analysis group deposition -- Crystal Structure of COVID-19 main protease in complex with Z219104216 |
| 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: 112.665 Å | b: 52.848 Å | c: 52.848 Å | α: 90.00° | β: 102.97° | γ: 90.00° |
| Resolution | 1.31 Å | Reflections | 53593 | Test set | 2605 (4.9%) | ||
| R | 0.1803 | R-free | 0.2116 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.31 Å | Reflections | 53593 | Test set | 2605 (4.9%) | ||
| Twin | false | Radiation damage | 7 | ||||
| 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 | 0.2420 | 0.1990 |
| R-free | 0.2552 | 0.2204 |
| Bond length RMS Z-score | 1.281 | 0.274 |
| Bond angle RMS Z-score | 1.002 | 0.534 |
| Model quality | ||
| Ramachandran plot normality | -1.212 49 | -0.457 71 |
| Rotamer normality | -0.800 76 | 0.371 94 |
| Coarse packing | 0.463 69 | 0.518 71 |
| Fine packing | -1.547 30 | -1.440 34 |
| Bump severity | 0.005 72 | 0.003 81 |
| Hydrogen bond satisfaction | 0.879 28 | 0.877 26 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 6 |
| Side chains flipped | 0 |
| Waters removed | 27 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 90 |
| Residues fitting density worse | 0 |