| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102615 |
| 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: 112.552Å b: 52.739Å c: 44.111Å | α: 90.00° β: 102.71° γ: 90.00° | ||
| Resolution | 1.88 Å | Reflections | 20602 | Test set | 1051 (5.1%) |
| R | 0.1872 | R-free | 0.2526 | ||
| According to PDB-REDO | |||||
| Resolution | 1.88 Å | Reflections | 20602 | Test set | 1051 (5.1%) |
| Twin | false | Radiation damage | 8 | ||
| 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 | 0.1967 | 0.2055 |
| R-free | 0.2592 | 0.2580 |
| Bond length RMS Z-score | 1.342 | 0.295 |
| Bond angle RMS Z-score | 1.045 | 0.519 |
| Model quality | ||
| Ramachandran plot normality | -2.243 27 | -1.949 32 |
| Rotamer normality | -2.250 46 | -0.916 74 |
| Coarse packing | 0.488 70 | 0.462 69 |
| Fine packing | -0.543 70 | -0.553 69 |
| MolProbity Clashscore | 5.900 45 | 3.580 68 |
| Hydrogen bond satisfaction | 0.869 21 | 0.869 21 |
| 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 |