| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z31432226 |
| 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: 111.604Å b: 52.401Å c: 44.322Å | α: 90.00° β: 102.78° γ: 90.00° | ||
| Resolution | 1.63 Å | Reflections | 30744 | Test set | 1513 (4.9%) |
| R | 0.1852 | R-free | 0.2282 | ||
| According to PDB-REDO | |||||
| Resolution | 1.63 Å | Reflections | 30744 | Test set | 1513 (4.9%) |
| Twin | false | Radiation damage | 12 | ||
| 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 | 0.2594 | 0.2220 |
| R-free | 0.2835 | 0.2634 |
| Bond length RMS Z-score | 1.301 | 0.416 |
| Bond angle RMS Z-score | 0.967 | 0.612 |
| Model quality | ||
| Ramachandran plot normality | -1.685 38 | -1.258 48 |
| Rotamer normality | -0.812 76 | -0.389 84 |
| Coarse packing | 0.509 70 | 0.442 68 |
| Fine packing | -0.359 75 | -0.457 72 |
| MolProbity Clashscore | 5.170 51 | 4.770 55 |
| Hydrogen bond satisfaction | 0.791 5 | 0.785 4 |
| 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 | 6 |
| Residues fitting density worse | 0 |