| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102372 |
| 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: 113.335 Å | b: 53.266 Å | c: 44.411 Å | α: 90.00° | β: 103.18° | γ: 90.00° |
| Resolution | 2.32 Å | Reflections | 11232 | Test set | 576 (5.1%) | ||
| R | 0.2121 | R-free | 0.3065 | ||||
| According to PDB-REDO | |||||||
| Resolution | 2.32 Å | Reflections | 11232 | Test set | 576 (5.1%) | ||
| Twin | false | Radiation damage | 29 | ||||
| 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 | 0.2287 | 0.2276 |
| R-free | 0.3046 | 0.3093 |
| Bond length RMS Z-score | 1.316 | 0.195 |
| Bond angle RMS Z-score | 0.926 | 0.442 |
| Model quality | ||
| Ramachandran plot normality | -3.003 17 | -2.980 17 |
| Rotamer normality | -2.628 39 | -2.331 44 |
| Coarse packing | -0.044 47 | -0.081 45 |
| Fine packing | -0.832 60 | -1.050 51 |
| MolProbity Clashscore | 3.480 69 | 6.130 44 |
| Hydrogen bond satisfaction | 0.833 10 | 0.832 9 |
| 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 |