| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102578 |
| 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: 112.394 Å | b: 52.591 Å | c: 44.385 Å | α: 90.00° | β: 103.04° | γ: 90.00° |
| Resolution | 1.88 Å | Reflections | 20647 | Test set | 1051 (5.1%) | ||
| R | 0.1676 | R-free | 0.2268 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.88 Å | Reflections | 20647 | Test set | 1051 (5.1%) | ||
| Twin | false | Radiation damage | 28 | ||||
| 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 | 0.1742 | 0.1781 |
| R-free | 0.2294 | 0.2278 |
| Bond length RMS Z-score | 1.261 | 0.293 |
| Bond angle RMS Z-score | 0.991 | 0.525 |
| Model quality | ||
| Ramachandran plot normality | -1.218 49 | -1.022 55 |
| Rotamer normality | -0.986 72 | -0.021 89 |
| Coarse packing | 0.682 77 | 0.623 74 |
| Fine packing | -0.366 75 | -0.363 75 |
| Bump severity | 0.005 72 | 0.010 56 |
| Hydrogen bond satisfaction | 0.870 22 | 0.875 25 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 5 |
| Side chains flipped | 0 |
| Waters removed | 47 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |