PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102972 |
This entry was created with PDB-REDO version 8.13 using the deposited PDB model version 1.5 |
From original header | |||||||
---|---|---|---|---|---|---|---|
Spacegroup | C 1 2 1 | a: 111.986 Å | b: 52.546 Å | c: 44.593 Å | α: 90.00° | β: 103.15° | γ: 90.00° |
Resolution | 1.83 Å | Reflections | 21541 | Test set | 1090 (5.1%) | ||
R | 0.2049 | R-free | 0.2775 | ||||
According to PDB-REDO | |||||||
Resolution | 1.83 Å | Reflections | 21541 | Test set | 1090 (5.1%) | ||
Twin | false | Radiation damage | 13 | ||||
PDB-REDO files | |||||||
Re-refined and rebuilt structure | Re-refined (only) structure |
All files
(compressed) |
|||||
Links | |||||||
PDBe | RCSB PDB | 3D bionotes | Proteopedia |
Original | PDB-REDO | |
---|---|---|
Crystallographic refinement | ||
R | 0.2175 | 0.2279 |
R-free | 0.2812 | 0.2788 |
Bond length RMS Z-score | 1.318 | 0.172 |
Bond angle RMS Z-score | 0.995 | 0.418 |
Model quality | ||
Ramachandran plot normality | -2.408 24 | -2.071 30 |
Rotamer normality | -2.379 43 | -1.190 68 |
Coarse packing | 0.260 61 | 0.193 58 |
Fine packing | -0.698 65 | -0.623 67 |
Bump severity | 0.015 45 | 0.007 65 |
Hydrogen bond satisfaction | 0.868 21 | 0.858 16 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 7 |
Side chains flipped | 0 |
Waters removed | 50 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |