| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z2856434836 |
| This entry was created with PDB-REDO version 8.20 using the deposited PDB model version 1.6 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.706 Å | b: 52.645 Å | c: 44.480 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 | 0.2055 |
| R-free | 0.2513 | 0.2579 |
| Bond length RMS Z-score | 1.275 | 0.186 |
| Bond angle RMS Z-score | 0.960 | 0.455 |
| Model quality | ||
| Ramachandran plot normality | -1.133 52 | -0.997 55 |
| Rotamer normality | -1.396 64 | -0.202 87 |
| Coarse packing | 0.388 66 | 0.279 62 |
| Fine packing | -0.425 73 | -0.477 72 |
| MolProbity Clashscore | 9.500 26 | 5.740 47 |
| Hydrogen bond satisfaction | 0.822 8 | 0.814 7 |
| 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 | 3 |
| Residues fitting density worse | 0 |