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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z2856434836 |
| This entry was created with PDB-REDO version 8.07 using the deposited PDB model version 1.5 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.706 Å | b: 52.645 Å | c: 52.645 Å | α: 90.00° | β: 102.87° | γ: 90.00° |
| Resolution | 1.72 Å | Reflections | 26626 | Test set | 1312 (4.9%) | ||
| R | 0.1672 | R-free | 0.2248 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.72 Å | Reflections | 26626 | Test set | 1312 (4.9%) | ||
| Twin | false | Radiation damage | 11 | ||||
| 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 | 0.2026 | 0.2053 |
| R-free | 0.2514 | 0.2568 |
| Bond length RMS Z-score | 1.275 | 0.185 |
| Bond angle RMS Z-score | 0.954 | 0.454 |
| Model quality | ||
| Ramachandran plot normality | -1.133 52 | -1.054 54 |
| Rotamer normality | -1.396 64 | -0.273 86 |
| Coarse packing | 0.388 66 | 0.288 62 |
| Fine packing | -1.684 24 | -1.441 34 |
| Bump severity | 0.012 51 | 0.014 47 |
| Hydrogen bond satisfaction | 0.837 10 | 0.821 8 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 9 |
| Side chains flipped | 0 |
| Waters removed | 134 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 3 |
| Residues fitting density worse | 0 |