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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1129283193 |
| 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: 111.643 Å | b: 52.352 Å | c: 52.352 Å | α: 90.00° | β: 103.08° | γ: 90.00° |
| Resolution | 1.88 Å | Reflections | 20087 | Test set | 1030 (5.1%) | ||
| R | 0.1991 | R-free | 0.2664 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.88 Å | Reflections | 20087 | Test set | 1030 (5.1%) | ||
| Twin | false | Radiation damage | 18 | ||||
| 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 | 0.2071 | 0.2122 |
| R-free | 0.2695 | 0.2735 |
| Bond length RMS Z-score | 1.300 | 0.233 |
| Bond angle RMS Z-score | 0.986 | 0.471 |
| Model quality | ||
| Ramachandran plot normality | -2.653 21 | -2.104 29 |
| Rotamer normality | -2.052 50 | -0.775 77 |
| Coarse packing | 0.692 77 | 0.543 72 |
| Fine packing | -1.644 26 | -1.382 37 |
| Bump severity | 0.014 47 | 0.008 62 |
| Hydrogen bond satisfaction | 0.888 36 | 0.882 30 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 10 |
| Side chains flipped | 0 |
| Waters removed | 58 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |