| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z2856434899 |
| 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: 113.212 Å | b: 53.034 Å | c: 44.302 Å | α: 90.00° | β: 102.95° | γ: 90.00° |
| Resolution | 1.68 Å | Reflections | 29081 | Test set | 1434 (4.9%) | ||
| R | 0.1755 | R-free | 0.2237 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.68 Å | Reflections | 29081 | Test set | 1434 (4.9%) | ||
| Twin | false | Radiation damage | 7 | ||||
| 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 | 0.1836 | 0.1858 |
| R-free | 0.2283 | 0.2276 |
| Bond length RMS Z-score | 1.420 | 0.622 |
| Bond angle RMS Z-score | 1.006 | 0.741 |
| Model quality | ||
| Ramachandran plot normality | -1.115 52 | -0.997 55 |
| Rotamer normality | -1.200 68 | -0.459 83 |
| Coarse packing | 0.470 69 | 0.430 68 |
| Fine packing | -0.410 74 | -0.379 74 |
| MolProbity Clashscore | 5.480 49 | 4.210 61 |
| Hydrogen bond satisfaction | 0.870 22 | 0.879 28 |
| 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 | 2 |
| Residues fitting density worse | 0 |