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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1220452176 |
| This entry was created with PDB-REDO version 8.07 using the deposited PDB model version 2.4 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.090 Å | b: 52.513 Å | c: 52.513 Å | α: 90.00° | β: 102.94° | γ: 90.00° |
| Resolution | 1.59 Å | Reflections | 33532 | Test set | 1657 (4.9%) | ||
| R | 0.1895 | R-free | 0.2330 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.59 Å | Reflections | 33532 | Test set | 1657 (4.9%) | ||
| 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 | 0.2116 | 0.2111 |
| R-free | 0.2553 | 0.2538 |
| Bond length RMS Z-score | 1.309 | 0.747 |
| Bond angle RMS Z-score | 0.973 | 0.776 |
| Model quality | ||
| Ramachandran plot normality | -1.424 44 | -1.065 54 |
| Rotamer normality | -1.235 67 | -0.710 78 |
| Coarse packing | 0.608 74 | 0.506 70 |
| Fine packing | -1.574 29 | -1.330 39 |
| Bump severity | 0.007 65 | 0.011 54 |
| Hydrogen bond satisfaction | 0.878 27 | 0.883 31 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 8 |
| Side chains flipped | 0 |
| Waters removed | 64 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |