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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0103067 |
| This entry was created with PDB-REDO version 7.34. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.164 Å | b: 52.739 Å | c: 44.481 Å | α: 90.00° | β: 102.96° | γ: 90.00° |
| Resolution | 1.80 Å | Reflections | 23575 | Test set | 1177 (5.0%) | ||
| R | 0.1860 | R-free | 0.2410 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.80 Å | Reflections | 23575 | Test set | 1177 (5.0%) | 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 | 0.1942 | 0.1972 |
| R-free | 0.2460 | 0.2419 |
| Bond length RMS Z-score | 0.650 | 0.383 |
| Bond angle RMS Z-score | 1.028 | 0.666 |
| Model quality | ||
| Ramachandran plot normality | -2.065 28 | -1.735 35 |
| Rotamer normality | -1.391 70 | -0.640 83 |
| Coarse packing | -0.267 48 | -0.304 46 |
| Fine packing | -1.483 32 | -1.305 40 |
| Bump severity | 0.004 78 | 0.001 92 |
| Hydrogen bond satisfaction | 0.891 39 | 0.888 36 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 7 |
| Side chains flipped | 0 |
| Waters removed | 55 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |