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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102615 |
| This entry was created with PDB-REDO version 7.36. |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.552 Å | b: 52.739 Å | c: 44.111 Å | α: 90.00° | β: 102.71° | γ: 90.00° |
| Resolution | 1.88 Å | Reflections | 20602 | Test set | 1051 (5.1%) | ||
| R | 0.1870 | R-free | 0.2530 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.88 Å | Reflections | 20602 | Test set | 1051 (5.1%) | ||
| 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 | 0.1968 | 0.2420 |
| R-free | 0.2592 | 0.2930 |
| Bond length RMS Z-score | 0.706 | 0.529 |
| Bond angle RMS Z-score | 1.076 | 0.777 |
| Model quality | ||
| Ramachandran plot normality | -2.392 23 | -2.698 19 |
| Rotamer normality | -2.249 53 | -2.170 55 |
| Coarse packing | -0.287 47 | -0.354 43 |
| Fine packing | -1.460 33 | -1.382 37 |
| Bump severity | 0.010 58 | 0.008 64 |
| Hydrogen bond satisfaction | 0.868 20 | 0.891 39 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 0 |
| Waters removed | 117 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 1 |