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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102275 |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 1.5 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.161 Å | b: 52.566 Å | c: 44.585 Å | α: 90.00° | β: 102.91° | γ: 90.00° |
| Resolution | 1.55 Å | Reflections | 36535 | Test set | 1797 (4.9%) | ||
| R | 0.1848 | R-free | 0.2236 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.55 Å | Reflections | 36535 | Test set | 1797 (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 | 3D bionotes | Proteopedia | ||||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.1947 | 0.1930 |
| R-free | 0.2320 | 0.2306 |
| Bond length RMS Z-score | 1.288 | 0.345 |
| Bond angle RMS Z-score | 1.003 | 0.566 |
| Model quality | ||
| Ramachandran plot normality | -1.062 54 | -1.057 54 |
| Rotamer normality | -0.776 77 | 0.000 90 |
| Coarse packing | 0.493 70 | 0.463 69 |
| Fine packing | -0.512 71 | -0.372 75 |
| Bump severity | 0.008 62 | 0.004 76 |
| Hydrogen bond satisfaction | 0.872 23 | 0.882 30 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 5 |
| Side chains built | 0 |
| Waters removed | 35 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 1 |
| Residues fitting density worse | 0 |