| 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 8.13 using the deposited PDB model version 1.5 |
| 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 | 0.1779 | R-free | 0.2572 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.06 Å | Reflections | 16048 | Test set | 821 (5.1%) | ||
| Twin | false | Radiation damage | 22 | ||||
| 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 | 0.1862 | 0.1996 |
| R-free | 0.2662 | 0.2618 |
| Bond length RMS Z-score | 1.347 | 0.168 |
| Bond angle RMS Z-score | 1.020 | 0.405 |
| Model quality | ||
| Ramachandran plot normality | -1.886 33 | -1.268 48 |
| Rotamer normality | -2.354 44 | -0.362 84 |
| Coarse packing | 0.303 63 | 0.193 58 |
| Fine packing | -0.746 63 | -0.714 64 |
| Bump severity | 0.003 81 | 0.003 81 |
| Hydrogen bond satisfaction | 0.860 17 | 0.863 18 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 7 |
| Side chains flipped | 0 |
| Waters removed | 66 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |