| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102241 |
| 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: 112.568 Å | b: 52.860 Å | c: 44.490 Å | α: 90.00° | β: 102.90° | γ: 90.00° |
| Resolution | 1.72 Å | Reflections | 26954 | Test set | 1330 (4.9%) | ||
| R | 0.1900 | R-free | 0.2405 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.72 Å | Reflections | 26954 | Test set | 1330 (4.9%) | ||
| Twin | false | Radiation damage | 21 | ||||
| PDB-REDO files | |||||||
| Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
|||||
| Links | |||||||
| PDBe | RCSB PDB | 3D bionotes | Proteopedia | ||||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.1991 | 0.1997 |
| R-free | 0.2479 | 0.2439 |
| Bond length RMS Z-score | 1.288 | 0.335 |
| Bond angle RMS Z-score | 0.992 | 0.574 |
| Model quality | ||
| Ramachandran plot normality | -1.499 42 | -1.193 50 |
| Rotamer normality | -1.169 68 | -0.199 87 |
| Coarse packing | 0.464 69 | 0.420 67 |
| Fine packing | -0.525 70 | -0.460 72 |
| Bump severity | 0.003 81 | 0.003 81 |
| Hydrogen bond satisfaction | 0.878 27 | 0.874 24 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 6 |
| Side chains flipped | 0 |
| Waters removed | 35 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |