| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102704 |
| 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: 112.943Å b: 52.908Å c: 44.529Å | α: 90.00° β: 103.09° γ: 90.00° | ||
| Resolution | 1.78 Å | Reflections | 24602 | Test set | 1226 (5.0%) |
| R | 0.1920 | R-free | 0.2474 | ||
| According to PDB-REDO | |||||
| Resolution | 1.78 Å | Reflections | 24602 | Test set | 1226 (5.0%) |
| Twin | false | Radiation damage | 30 | ||
| 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 | 0.2096 | 0.2069 |
| R-free | 0.2594 | 0.2563 |
| Bond length RMS Z-score | 1.287 | 0.341 |
| Bond angle RMS Z-score | 0.963 | 0.555 |
| Model quality | ||
| Ramachandran plot normality | -1.808 35 | -1.452 43 |
| Rotamer normality | -1.373 64 | -0.490 82 |
| Coarse packing | 0.396 66 | 0.333 64 |
| Fine packing | -0.626 67 | -0.565 69 |
| MolProbity Clashscore | 5.050 53 | 5.260 51 |
| Hydrogen bond satisfaction | 0.876 26 | 0.877 26 |
| 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 | 0 |
| Residues fitting density worse | 0 |