| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z2737076969 |
| 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: 112.962 Å | b: 52.752 Å | c: 44.174 Å | α: 90.00° | β: 102.99° | γ: 90.00° |
| Resolution | 1.81 Å | Reflections | 23138 | Test set | 1164 (5.0%) | ||
| R | 0.1903 | R-free | 0.2483 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.81 Å | Reflections | 23138 | Test set | 1164 (5.0%) | ||
| Twin | false | Radiation damage | 7 | ||||
| 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 | 0.2057 | 0.2136 |
| R-free | 0.2580 | 0.2566 |
| Bond length RMS Z-score | 1.349 | 0.214 |
| Bond angle RMS Z-score | 1.005 | 0.467 |
| Model quality | ||
| Ramachandran plot normality | -1.972 32 | -1.553 41 |
| Rotamer normality | -1.955 52 | -0.544 81 |
| Coarse packing | 0.461 69 | 0.384 66 |
| Fine packing | -0.444 73 | -0.557 69 |
| MolProbity Clashscore | 6.320 42 | 4.000 63 |
| Hydrogen bond satisfaction | 0.866 20 | 0.865 19 |
| 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 | 1 |