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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102539 |
| This entry was created with PDB-REDO version 7.34. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 113.529 Å | b: 53.304 Å | c: 44.465 Å | α: 90.00° | β: 103.23° | γ: 90.00° |
| Resolution | 2.06 Å | Reflections | 16048 | Test set | 821 (5.1%) | ||
| R | 0.1780 | R-free | 0.2570 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.06 Å | Reflections | 16048 | Test set | 821 (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 | 0.1858 | 0.2052 |
| R-free | 0.2655 | 0.2630 |
| Bond length RMS Z-score | 0.699 | 0.387 |
| Bond angle RMS Z-score | 1.059 | 0.654 |
| Model quality | ||
| Ramachandran plot normality | -2.043 29 | -1.568 38 |
| Rotamer normality | -2.353 51 | -1.241 73 |
| Coarse packing | -0.434 39 | -0.428 40 |
| Fine packing | -1.655 25 | -1.560 29 |
| Bump severity | 0.008 64 | 0.003 82 |
| Hydrogen bond satisfaction | 0.875 25 | 0.891 39 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 10 |
| Side chains flipped | 0 |
| Waters removed | 68 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |