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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102287 |
| This entry was created with PDB-REDO version 7.34 using the deposited PDB model |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.639 Å | b: 53.038 Å | c: 44.943 Å | α: 90.00° | β: 102.71° | γ: 90.00° |
| Resolution | 2.07 Å | Reflections | 15821 | Test set | 808 (5.1%) | ||
| R | 0.1750 | R-free | 0.2510 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.07 Å | Reflections | 15821 | Test set | 808 (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 | 0.1850 | 0.2049 |
| R-free | 0.2578 | 0.2624 |
| Bond length RMS Z-score | 0.662 | 0.412 |
| Bond angle RMS Z-score | 1.015 | 0.676 |
| Model quality | ||
| Ramachandran plot normality | -2.181 26 | -2.061 28 |
| Rotamer normality | -2.305 52 | -1.936 59 |
| Coarse packing | -0.388 42 | -0.295 46 |
| Fine packing | -1.586 28 | -1.221 44 |
| Bump severity | 0.015 47 | 0.003 82 |
| Hydrogen bond satisfaction | 0.891 39 | 0.892 40 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 4 |
| Side chains flipped | 0 |
| Waters removed | 148 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 1 |