| 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 8.13 using the deposited PDB model version 1.5 |
| 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 | 0.2067 | R-free | 0.2968 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.03 Å | Reflections | 16595 | Test set | 848 (5.1%) | ||
| Twin | false | Radiation damage | 18 | ||||
| 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 | 0.2136 | 0.2166 |
| R-free | 0.2943 | 0.2842 |
| Bond length RMS Z-score | 1.315 | 0.219 |
| Bond angle RMS Z-score | 0.993 | 0.467 |
| Model quality | ||
| Ramachandran plot normality | -3.084 16 | -2.194 28 |
| Rotamer normality | -1.704 57 | -0.817 76 |
| Coarse packing | 0.198 58 | 0.215 59 |
| Fine packing | -0.674 65 | -0.731 63 |
| Bump severity | 0.017 42 | 0.009 59 |
| Hydrogen bond satisfaction | 0.855 15 | 0.855 15 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 0 |
| Waters removed | 55 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |