| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102575 |
| This entry was created with PDB-REDO version 8.20 using the deposited PDB model version 1.6 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.854 Å | b: 52.919 Å | c: 44.942 Å | α: 90.00° | β: 103.14° | γ: 90.00° |
| Resolution | 1.75 Å | Reflections | 25961 | Test set | 1294 (5.0%) | ||
| R | 0.1875 | R-free | 0.2348 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.75 Å | Reflections | 25961 | Test set | 1294 (5.0%) | ||
| Twin | false | Radiation damage | 13 | ||||
| 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 | 0.1968 | 0.2035 |
| R-free | 0.2398 | 0.2369 |
| Bond length RMS Z-score | 1.320 | 0.320 |
| Bond angle RMS Z-score | 0.986 | 0.540 |
| Model quality | ||
| Ramachandran plot normality | -1.566 40 | -1.211 49 |
| Rotamer normality | -1.547 60 | -0.462 83 |
| Coarse packing | 0.178 57 | 0.126 55 |
| Fine packing | -0.816 60 | -0.866 58 |
| MolProbity Clashscore | 5.680 47 | 4.420 59 |
| Hydrogen bond satisfaction | 0.871 22 | 0.870 22 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | N/A |
| Side chains built | 0 |
| Waters removed | N/A |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |