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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z126932614 |
| This entry was created with PDB-REDO version 8.07 using the deposited PDB model version 1.5 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 111.952 Å | b: 52.630 Å | c: 52.630 Å | α: 90.00° | β: 102.98° | γ: 90.00° |
| Resolution | 1.41 Å | Reflections | 45835 | Test set | 2211 (4.8%) | ||
| R | 0.1776 | R-free | 0.2110 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.41 Å | Reflections | 45835 | Test set | 2211 (4.8%) | ||
| Twin | false | Radiation damage | 30 | ||||
| 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 | 0.1857 | 0.1859 |
| R-free | 0.2175 | 0.2166 |
| Bond length RMS Z-score | 1.302 | 0.414 |
| Bond angle RMS Z-score | 1.004 | 0.614 |
| Model quality | ||
| Ramachandran plot normality | -0.370 73 | -0.342 74 |
| Rotamer normality | 0.035 90 | 0.668 96 |
| Coarse packing | 0.516 71 | 0.484 70 |
| Fine packing | -1.530 30 | -1.441 34 |
| Bump severity | 0.006 68 | 0.005 72 |
| Hydrogen bond satisfaction | 0.889 37 | 0.894 42 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 3 |
| Side chains flipped | 0 |
| Waters removed | 42 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 1 |