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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102190 |
| This entry was created with PDB-REDO version 7.36 using the deposited PDB model |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 114.135 Å | b: 53.675 Å | c: 44.208 Å | α: 90.00° | β: 100.86° | γ: 90.00° |
| Resolution | 2.03 Å | Reflections | 16595 | Test set | 848 (5.1%) | ||
| R | 0.2070 | R-free | 0.2970 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.03 Å | Reflections | 16595 | Test set | 848 (5.1%) | ||
| Twin | false | Radiation damage | N/A | ||||
| 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 | 0.2135 | 0.2083 |
| R-free | 0.2951 | 0.2859 |
| Bond length RMS Z-score | 0.672 | 0.531 |
| Bond angle RMS Z-score | 1.034 | 0.784 |
| Model quality | ||
| Ramachandran plot normality | -3.253 14 | -2.985 16 |
| Rotamer normality | -1.705 64 | -3.184 37 |
| Coarse packing | -0.482 37 | -0.429 40 |
| Fine packing | -1.776 21 | -1.711 23 |
| Bump severity | 0.017 44 | 0.009 61 |
| Hydrogen bond satisfaction | 0.875 25 | 0.867 20 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 9 |
| Side chains flipped | 0 |
| Waters removed | 55 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 1 |
| Residues fitting density worse | 0 |