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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z18197050 |
| This entry was created with PDB-REDO version 8.07 using the deposited PDB model version 2.4 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.891 Å | b: 53.030 Å | c: 53.030 Å | α: 90.00° | β: 102.46° | γ: 90.00° |
| Resolution | 1.93 Å | Reflections | 19175 | Test set | 991 (5.2%) | ||
| R | 0.1730 | R-free | 0.2346 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.93 Å | Reflections | 19175 | Test set | 991 (5.2%) | ||
| Twin | false | Radiation damage | 19 | ||||
| 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 | 0.1823 | 0.1884 |
| R-free | 0.2417 | 0.2439 |
| Bond length RMS Z-score | 1.310 | 0.374 |
| Bond angle RMS Z-score | 0.996 | 0.584 |
| Model quality | ||
| Ramachandran plot normality | -1.767 36 | -1.464 43 |
| Rotamer normality | -2.143 48 | -1.120 70 |
| Coarse packing | 0.421 67 | 0.501 70 |
| Fine packing | -1.521 31 | -1.188 45 |
| Bump severity | 0.006 68 | 0.010 56 |
| Hydrogen bond satisfaction | 0.885 33 | 0.887 35 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 9 |
| Side chains flipped | 0 |
| Waters removed | 112 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 1 |
| Residues fitting density worse | 0 |