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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1129283193 |
| This entry was created with PDB-REDO version 7.34. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 111.643 Å | b: 52.352 Å | c: 44.369 Å | α: 90.00° | β: 103.08° | γ: 90.00° |
| Resolution | 1.88 Å | Reflections | 20087 | Test set | 1030 (5.1%) | ||
| R | 0.1990 | R-free | 0.2660 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.88 Å | Reflections | 20087 | Test set | 1030 (5.1%) | Twin | false |
| 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 | 0.2072 | 0.2190 |
| R-free | 0.2700 | 0.2770 |
| Bond length RMS Z-score | 0.655 | 0.345 |
| Bond angle RMS Z-score | 1.035 | 0.620 |
| Model quality | ||
| Ramachandran plot normality | -2.884 17 | -2.387 23 |
| Rotamer normality | -2.053 57 | -1.038 77 |
| Coarse packing | -0.178 52 | -0.247 49 |
| Fine packing | -1.614 27 | -1.331 39 |
| Bump severity | 0.014 49 | 0.010 58 |
| Hydrogen bond satisfaction | 0.885 33 | 0.882 30 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 9 |
| Side chains flipped | 0 |
| Waters removed | 66 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |