| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102615 |
| 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: 112.552 Å | b: 52.739 Å | c: 44.111 Å | α: 90.00° | β: 102.71° | γ: 90.00° |
| Resolution | 1.88 Å | Reflections | 20602 | Test set | 1051 (5.1%) | ||
| R | 0.1872 | R-free | 0.2526 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.88 Å | Reflections | 20602 | Test set | 1051 (5.1%) | ||
| Twin | false | Radiation damage | 10 | ||||
| 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 | 0.1969 | 0.2038 |
| R-free | 0.2591 | 0.2639 |
| Bond length RMS Z-score | 1.342 | 0.198 |
| Bond angle RMS Z-score | 1.045 | 0.450 |
| Model quality | ||
| Ramachandran plot normality | -2.243 27 | -1.835 34 |
| Rotamer normality | -2.250 46 | -0.878 75 |
| Coarse packing | 0.488 70 | 0.411 67 |
| Fine packing | -0.543 70 | -0.487 71 |
| Bump severity | 0.009 59 | 0.007 65 |
| Hydrogen bond satisfaction | 0.869 21 | 0.870 22 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 7 |
| Side chains flipped | 0 |
| Waters removed | 70 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |