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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z2737076969 |
| 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: 112.962 Å | b: 52.752 Å | c: 52.752 Å | α: 90.00° | β: 102.99° | γ: 90.00° |
| Resolution | 1.81 Å | Reflections | 23138 | Test set | 1164 (5.0%) | ||
| R | 0.1903 | R-free | 0.2483 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.81 Å | Reflections | 23138 | Test set | 1164 (5.0%) | ||
| 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 | 0.2057 | 0.2137 |
| R-free | 0.2580 | 0.2565 |
| Bond length RMS Z-score | 1.349 | 0.214 |
| Bond angle RMS Z-score | 0.999 | 0.470 |
| Model quality | ||
| Ramachandran plot normality | -1.972 32 | -1.468 43 |
| Rotamer normality | -1.955 52 | -0.693 78 |
| Coarse packing | 0.461 69 | 0.389 66 |
| Fine packing | -1.591 28 | -1.358 38 |
| Bump severity | 0.006 68 | 0.005 72 |
| Hydrogen bond satisfaction | 0.876 26 | 0.894 42 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 11 |
| Side chains flipped | 0 |
| Waters removed | 93 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 1 |