| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102974 |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 1.5 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 111.969 Å | b: 52.541 Å | c: 44.676 Å | α: 90.00° | β: 103.08° | γ: 90.00° |
| Resolution | 1.90 Å | Reflections | 19552 | Test set | 1005 (5.1%) | ||
| R | 0.2098 | R-free | 0.2767 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.90 Å | Reflections | 19552 | Test set | 1005 (5.1%) | ||
| Twin | false | Radiation damage | 43 | ||||
| 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 | 0.2218 | 0.2279 |
| R-free | 0.2836 | 0.2810 |
| Bond length RMS Z-score | 1.283 | 0.183 |
| Bond angle RMS Z-score | 0.946 | 0.435 |
| Model quality | ||
| Ramachandran plot normality | -3.084 16 | -2.769 19 |
| Rotamer normality | -2.283 45 | -1.163 69 |
| Coarse packing | 0.316 63 | 0.224 59 |
| Fine packing | -0.789 61 | -0.769 62 |
| Bump severity | 0.014 47 | 0.019 39 |
| Hydrogen bond satisfaction | 0.869 21 | 0.853 15 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 11 |
| Side chains flipped | 0 |
| Waters removed | 69 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |