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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0103072 |
| This entry was created with PDB-REDO version 7.34 using the deposited PDB model |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.220 Å | b: 52.787 Å | c: 44.460 Å | α: 90.00° | β: 102.96° | γ: 90.00° |
| Resolution | 1.60 Å | Reflections | 32865 | Test set | 1627 (5.0%) | ||
| R | 0.1760 | R-free | 0.2220 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.60 Å | Reflections | 32865 | Test set | 1627 (5.0%) | ||
| 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 | 0.1836 | 0.2419 |
| R-free | 0.2294 | 0.2915 |
| Bond length RMS Z-score | 0.666 | 0.705 |
| Bond angle RMS Z-score | 1.014 | 0.894 |
| Model quality | ||
| Ramachandran plot normality | -1.200 47 | -1.771 34 |
| Rotamer normality | -0.689 83 | -1.730 63 |
| Coarse packing | -0.155 54 | -0.311 46 |
| Fine packing | -1.559 29 | -1.328 39 |
| Bump severity | 0.006 70 | 0.010 58 |
| Hydrogen bond satisfaction | 0.900 50 | 0.882 30 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 0 |
| Waters removed | 40 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 14 |