| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102201 |
| This entry was created with PDB-REDO version 8.20 using the deposited PDB model version 1.6 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.074 Å | b: 52.597 Å | c: 44.389 Å | α: 90.00° | β: 102.86° | γ: 90.00° |
| Resolution | 1.81 Å | Reflections | 23004 | Test set | 1162 (5.1%) | ||
| R | 0.1783 | R-free | 0.2311 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.81 Å | Reflections | 23004 | Test set | 1162 (5.1%) | ||
| Twin | false | Radiation damage | 22 | ||||
| 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 | 0.1870 | 0.1962 |
| R-free | 0.2335 | 0.2332 |
| Bond length RMS Z-score | 1.276 | 0.175 |
| Bond angle RMS Z-score | 0.989 | 0.434 |
| Model quality | ||
| Ramachandran plot normality | -1.595 40 | -1.255 48 |
| Rotamer normality | -1.175 68 | 0.101 91 |
| Coarse packing | 0.495 70 | 0.413 67 |
| Fine packing | -0.600 68 | -0.426 73 |
| MolProbity Clashscore | 4.830 55 | 2.520 81 |
| Hydrogen bond satisfaction | 0.876 26 | 0.869 21 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | N/A |
| Side chains built | 0 |
| Waters removed | N/A |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |