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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102972 |
| This entry was created with PDB-REDO version 7.34. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 111.986 Å | b: 52.546 Å | c: 44.593 Å | α: 90.00° | β: 103.15° | γ: 90.00° |
| Resolution | 1.83 Å | Reflections | 21541 | Test set | 1090 (5.1%) | ||
| R | 0.2050 | R-free | 0.2780 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.83 Å | Reflections | 21541 | Test set | 1090 (5.1%) | Twin | false |
| 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 | 0.2172 | 0.2235 |
| R-free | 0.2821 | 0.2796 |
| Bond length RMS Z-score | 0.682 | 0.437 |
| Bond angle RMS Z-score | 1.048 | 0.689 |
| Model quality | ||
| Ramachandran plot normality | -2.583 21 | -2.247 25 |
| Rotamer normality | -2.379 51 | -1.717 63 |
| Coarse packing | -0.486 37 | -0.417 40 |
| Fine packing | -1.744 22 | -1.631 26 |
| Bump severity | 0.015 47 | 0.008 64 |
| Hydrogen bond satisfaction | 0.870 22 | 0.880 28 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 0 |
| Waters removed | 46 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |