| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1587220559 |
| 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: 112.398Å b: 52.720Å c: 44.400Å | α: 90.00° β: 102.89° γ: 90.00° | ||
| Resolution | 1.73 Å | Reflections | 26435 | Test set | 1314 (5.0%) |
| R | 0.1826 | R-free | 0.2371 | ||
| According to PDB-REDO | |||||
| Resolution | 1.73 Å | Reflections | 26435 | Test set | 1314 (5.0%) |
| Twin | false | Radiation damage | 37 | ||
| PDB-REDO files | |||||
| Re-refined and rebuilt structure |
Re-refined (only) structure
|
All files
(compressed) |
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| Links | |||||
| PDBe | RCSB PDB | Proteopedia | |||
| Original | PDB-REDO | |
|---|---|---|
| Crystallographic refinement | ||
| R | 0.1938 | 0.1963 |
| R-free | 0.2485 | 0.2410 |
| Bond length RMS Z-score | 1.324 | 0.311 |
| Bond angle RMS Z-score | 0.990 | 0.531 |
| Model quality | ||
| Ramachandran plot normality | -1.684 38 | -1.242 49 |
| Rotamer normality | -1.472 62 | -0.667 79 |
| Coarse packing | 0.461 69 | 0.383 66 |
| Fine packing | -0.556 69 | -0.624 67 |
| MolProbity Clashscore | 4.830 55 | 3.360 71 |
| Hydrogen bond satisfaction | 0.882 30 | 0.863 18 |
| 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 | 0 |