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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102243 |
| This entry was created with PDB-REDO version 7.34 using the deposited PDB model |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.828 Å | b: 53.056 Å | c: 44.493 Å | α: 90.00° | β: 103.19° | γ: 90.00° |
| Resolution | 1.43 Å | Reflections | 46157 | Test set | 2235 (4.8%) | ||
| R | 0.1900 | R-free | 0.2230 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.43 Å | Reflections | 46157 | Test set | 2235 (4.8%) | ||
| Twin | false | Radiation damage | N/A | ||||
| 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 | 0.2061 | 0.2027 |
| R-free | 0.2400 | 0.2310 |
| Bond length RMS Z-score | 0.662 | 0.429 |
| Bond angle RMS Z-score | 1.045 | 0.717 |
| Model quality | ||
| Ramachandran plot normality | -0.786 59 | -0.714 61 |
| Rotamer normality | -0.898 79 | 0.141 93 |
| Coarse packing | -0.277 47 | -0.249 49 |
| Fine packing | -1.550 29 | -1.432 34 |
| Bump severity | 0.004 78 | 0.013 51 |
| Hydrogen bond satisfaction | 0.874 24 | 0.885 33 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 10 |
| Side chains flipped | 0 |
| Waters removed | 38 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 2 |
| Residues fitting density worse | 0 |