| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102269 |
| 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: 112.889 Å | b: 53.003 Å | c: 44.457 Å | α: 90.00° | β: 103.04° | γ: 90.00° |
| Resolution | 1.68 Å | Reflections | 29092 | Test set | 1441 (5.0%) | ||
| R | 0.1820 | R-free | 0.2220 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.68 Å | Reflections | 29092 | Test set | 1441 (5.0%) | ||
| Twin | false | Radiation damage | 8 | ||||
| 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 | 0.1896 | 0.1956 |
| R-free | 0.2258 | 0.2300 |
| Bond length RMS Z-score | 1.294 | 0.422 |
| Bond angle RMS Z-score | 0.986 | 0.609 |
| Model quality | ||
| Ramachandran plot normality | -1.436 44 | -0.823 60 |
| Rotamer normality | -0.965 73 | -0.167 87 |
| Coarse packing | 0.444 68 | 0.430 68 |
| Fine packing | -0.480 72 | -0.439 73 |
| MolProbity Clashscore | 8.610 29 | 7.140 37 |
| Hydrogen bond satisfaction | 0.874 24 | 0.875 25 |
| 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 |