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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z33545544 |
| 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: 112.530 Å | b: 52.810 Å | c: 52.810 Å | α: 90.00° | β: 102.15° | γ: 90.00° |
| Resolution | 2.07 Å | Reflections | 15700 | Test set | 793 (5.1%) | ||
| R | 0.1811 | R-free | 0.2649 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.07 Å | Reflections | 15700 | Test set | 793 (5.1%) | ||
| Twin | false | Radiation damage | 20 | ||||
| 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 | 0.1895 | 0.2101 |
| R-free | 0.2684 | 0.2678 |
| Bond length RMS Z-score | 1.390 | 0.255 |
| Bond angle RMS Z-score | 1.005 | 0.501 |
| Model quality | ||
| Ramachandran plot normality | -2.676 21 | -1.967 32 |
| Rotamer normality | -2.334 44 | -1.036 71 |
| Coarse packing | 0.402 67 | 0.291 62 |
| Fine packing | -1.532 30 | -1.379 37 |
| Bump severity | 0.007 65 | 0.010 56 |
| Hydrogen bond satisfaction | 0.886 34 | 0.894 42 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 9 |
| Side chains flipped | 0 |
| Waters removed | 108 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |