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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z3241250482 |
| 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: 112.225 Å | b: 52.701 Å | c: 52.701 Å | α: 90.00° | β: 102.89° | γ: 90.00° |
| Resolution | 1.74 Å | Reflections | 26161 | Test set | 1302 (5.0%) | ||
| R | 0.1776 | R-free | 0.2306 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.74 Å | Reflections | 26161 | Test set | 1302 (5.0%) | ||
| Twin | false | Radiation damage | 3 | ||||
| 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 | 0.1867 | 0.1932 |
| R-free | 0.2370 | 0.2404 |
| Bond length RMS Z-score | 1.304 | 0.448 |
| Bond angle RMS Z-score | 0.982 | 0.619 |
| Model quality | ||
| Ramachandran plot normality | -1.466 43 | -1.102 53 |
| Rotamer normality | -0.997 72 | -0.110 88 |
| Coarse packing | 0.524 71 | 0.431 68 |
| Fine packing | -1.636 26 | -1.453 34 |
| Bump severity | 0.003 81 | 0.004 76 |
| Hydrogen bond satisfaction | 0.905 57 | 0.897 46 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 6 |
| Side chains flipped | 0 |
| Waters removed | 63 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |