| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0103067 |
| 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: 112.164 Å | b: 52.739 Å | c: 44.481 Å | α: 90.00° | β: 102.96° | γ: 90.00° |
| Resolution | 1.80 Å | Reflections | 23575 | Test set | 1177 (5.0%) | ||
| R | 0.1864 | R-free | 0.2414 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.80 Å | Reflections | 23575 | Test set | 1177 (5.0%) | ||
| Twin | false | Radiation damage | 49 | ||||
| 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 | 0.1944 | 0.1904 |
| R-free | 0.2457 | 0.2440 |
| Bond length RMS Z-score | 1.280 | 0.339 |
| Bond angle RMS Z-score | 0.983 | 0.570 |
| Model quality | ||
| Ramachandran plot normality | -1.838 34 | -1.633 39 |
| Rotamer normality | -1.391 64 | -0.528 81 |
| Coarse packing | 0.516 71 | 0.443 68 |
| Fine packing | -0.488 71 | -0.500 71 |
| Bump severity | 0.004 76 | 0.005 72 |
| Hydrogen bond satisfaction | 0.877 26 | 0.868 21 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 0 |
| Waters removed | 54 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |