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| 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 7.34. |
| 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 | 0.1680 | R-free | 0.2270 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.88 Å | Reflections | 20647 | Test set | 1051 (5.1%) | Twin | false |
| 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 | 0.2114 |
| R-free | 0.2297 | 0.2609 |
| Bond length RMS Z-score | 0.648 | 0.574 |
| Bond angle RMS Z-score | 1.033 | 0.808 |
| Model quality | ||
| Ramachandran plot normality | -1.407 42 | -2.341 24 |
| Rotamer normality | -0.986 78 | -1.346 71 |
| Coarse packing | -0.096 57 | -0.218 50 |
| Fine packing | -1.373 37 | -1.356 38 |
| Bump severity | 0.005 74 | 0.008 64 |
| Hydrogen bond satisfaction | 0.906 58 | 0.890 38 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 9 |
| Side chains flipped | 0 |
| Waters removed | 61 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 2 |