| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z979145504 |
| 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: 112.577Å b: 52.959Å c: 44.586Å | α: 90.00° β: 102.99° γ: 90.00° | ||
| Resolution | 1.40 Å | Reflections | 46629 | Test set | 2260 (4.8%) |
| R | 0.1795 | R-free | 0.2128 | ||
| According to PDB-REDO | |||||
| Resolution | 1.40 Å | Reflections | 46629 | Test set | 2260 (4.8%) |
| Twin | false | Radiation damage | 15 | ||
| 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 | 0.1851 | 0.1841 |
| R-free | 0.2177 | 0.2175 |
| Bond length RMS Z-score | 1.305 | 0.321 |
| Bond angle RMS Z-score | 1.021 | 0.577 |
| Model quality | ||
| Ramachandran plot normality | -0.323 75 | -0.301 75 |
| Rotamer normality | -0.303 85 | 0.731 96 |
| Coarse packing | 0.511 71 | 0.469 69 |
| Fine packing | -0.513 71 | -0.512 71 |
| MolProbity Clashscore | 4.340 60 | 4.340 60 |
| Hydrogen bond satisfaction | 0.878 27 | 0.875 25 |
| 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 | 2 |
| Residues fitting density worse | 0 |