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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1271660837 |
| 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: 112.489 Å | b: 52.630 Å | c: 52.630 Å | α: 90.00° | β: 102.98° | γ: 90.00° |
| Resolution | 1.48 Å | Reflections | 40538 | Test set | 2001 (4.9%) | ||
| R | 0.1833 | R-free | 0.2235 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.48 Å | Reflections | 40538 | Test set | 2001 (4.9%) | ||
| Twin | false | Radiation damage | 36 | ||||
| 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 | 0.1907 | 0.1940 |
| R-free | 0.2307 | 0.2317 |
| Bond length RMS Z-score | 1.292 | 0.583 |
| Bond angle RMS Z-score | 0.989 | 0.697 |
| Model quality | ||
| Ramachandran plot normality | -0.924 58 | -0.833 60 |
| Rotamer normality | -0.254 86 | 0.141 91 |
| Coarse packing | 0.532 71 | 0.490 70 |
| Fine packing | -1.507 31 | -1.448 34 |
| Bump severity | 0.005 72 | 0.009 59 |
| Hydrogen bond satisfaction | 0.901 51 | 0.911 65 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 6 |
| Side chains flipped | 0 |
| Waters removed | 50 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |