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| PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102121 |
| This entry was created with PDB-REDO version 7.36 using the deposited PDB model |
| From original header | |||||||
|---|---|---|---|---|---|---|---|
| Spacegroup | C 1 2 1 | a: 112.518 Å | b: 52.659 Å | c: 44.542 Å | α: 90.00° | β: 102.95° | γ: 90.00° |
| Resolution | 1.53 Å | Reflections | 37945 | Test set | 1854 (4.9%) | ||
| R | 0.1750 | R-free | 0.2100 | ||||
| According to PDB-REDO | |||||||
| Resolution | 1.53 Å | Reflections | 37945 | Test set | 1854 (4.9%) | ||
| Twin | false | Radiation damage | N/A | ||||
| 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 | 0.1815 | 0.2202 |
| R-free | 0.2133 | 0.2513 |
| Bond length RMS Z-score | 0.658 | 0.679 |
| Bond angle RMS Z-score | 1.031 | 0.879 |
| Model quality | ||
| Ramachandran plot normality | -1.069 51 | -1.301 45 |
| Rotamer normality | -0.658 83 | -0.895 79 |
| Coarse packing | -0.211 51 | -0.261 48 |
| Fine packing | -1.672 25 | -1.541 30 |
| Bump severity | 0.009 61 | 0.016 45 |
| Hydrogen bond satisfaction | 0.892 40 | 0.894 43 |
| WHAT_CHECK | Report | Report |
Kleywegt-like plot |
| Description | Count |
|---|---|
| Rotamers changed | 6 |
| Side chains flipped | 0 |
| Waters removed | 30 |
| Peptides flipped | 0 |
| Chiralities fixed | 0 |
| Residues fitting density better | 0 |
| Residues fitting density worse | 10 |