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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102911 |
| This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 1.5 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 113.335 Å | b: 53.297 Å | c: 44.517 Å | α: 90.00° | β: 103.12° | γ: 90.00° |
| Resolution | 1.96 Å | Reflections | 18577 | Test set | 965 (5.2%) | ||
| R | 0.1958 | R-free | 0.2735 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.96 Å | Reflections | 18577 | Test set | 965 (5.2%) | ||
| Twin | false | Radiation damage | 13 | ||||
| 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 | 0.2136 | 0.2168 |
| R-free | 0.2707 | 0.2670 |
| Bond length RMS Z-score | 1.298 | 0.167 |
| Bond angle RMS Z-score | 0.937 | 0.422 |
| Model quality | ||
| Ramachandran plot normality | -1.330 46 | -0.706 64 |
| Rotamer normality | -2.248 46 | -1.712 57 |
| Coarse packing | 0.286 62 | 0.258 61 |
| Fine packing | -0.536 70 | -0.592 68 |
| Bump severity | 0.005 72 | 0.015 45 |
| Hydrogen bond satisfaction | 0.859 17 | 0.852 14 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 7 |
| Side chains built | 0 |
| Waters removed | 67 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 0 |