| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1348371854 |
| This entry was created with PDB-REDO version 8.20 using the deposited PDB model version 1.6 |
| From original header | |||||
|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.714Å b: 52.798Å c: 44.574Å | α: 90.00° β: 103.04° γ: 90.00° | ||
| Resolution | 1.45 Å | Reflections | 43060 | Test set | 2102 (4.9%) |
| R | 0.1806 | R-free | 0.2174 | ||
| According to PDB-REDO | |||||
| Resolution | 1.45 Å | Reflections | 43060 | Test set | 2102 (4.9%) |
| Twin | false | Radiation damage | 34 | ||
| PDB-REDO files | |||||
| Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
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| Links | |||||
| PDBe | RCSB PDB | Proteopedia | |||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.1910 | 0.1863 |
| R-free | 0.2271 | 0.2259 |
| Bond length RMS Z-score | 1.295 | 0.993 |
| Bond angle RMS Z-score | 0.997 | 0.927 |
| Model quality | ||
| Ramachandran plot normality | -0.350 74 | -0.458 71 |
| Rotamer normality | -0.119 88 | 0.236 92 |
| Coarse packing | 0.559 72 | 0.479 69 |
| Fine packing | -0.435 73 | -0.570 69 |
| MolProbity Clashscore | 3.990 63 | 5.470 49 |
| Hydrogen bond satisfaction | 0.883 31 | 0.881 29 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | N/A |
| Side chains built | 0 |
| Waters removed | N/A |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 1 |
| Residues fitting density worse | 0 |