| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z18197050 |
| This entry was created with PDB-REDO version 8.20 using the deposited PDB model version 2.5 |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.891 Å | b: 53.030 Å | c: 44.352 Å | α: 90.00° | β: 102.46° | γ: 90.00° |
| Resolution | 1.93 Å | Reflections | 19175 | Test set | 991 (5.2%) | ||
| R | 0.1730 | R-free | 0.2346 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.93 Å | Reflections | 19175 | Test set | 991 (5.2%) | ||
| Twin | false | Radiation damage | 18 | ||||
| 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 | 0.1823 | 0.1911 |
| R-free | 0.2417 | 0.2452 |
| Bond length RMS Z-score | 1.309 | 0.385 |
| Bond angle RMS Z-score | 1.006 | 0.588 |
| Model quality | ||
| Ramachandran plot normality | -1.767 36 | -1.605 40 |
| Rotamer normality | -2.143 48 | -1.159 69 |
| Coarse packing | 0.421 67 | 0.496 70 |
| Fine packing | -0.343 75 | -0.489 71 |
| MolProbity Clashscore | 7.380 35 | 5.270 51 |
| Hydrogen bond satisfaction | 0.864 19 | 0.878 27 |
| 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 | 1 |
| Residues fitting density worse | 0 |