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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z2643472210 |
This entry was created with PDB-REDO version 7.34. |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 112.634 Å | b: 52.833 Å | c: 44.441 Å | α: 90.00° | β: 103.08° | γ: 90.00° |
Resolution | 1.52 Å | Reflections | 38237 | Test set | 1856 (4.9%) | ||
R | 0.1770 | R-free | 0.2150 | ||||
According to PDB-REDO | |||||||
Resolution | 1.52 Å | Reflections | 38237 | Test set | 1856 (4.9%) | Twin | false |
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 | 0.1856 | 0.2411 |
R-free | 0.2231 | 0.2818 |
Bond length RMS Z-score | 0.655 | 0.710 |
Bond angle RMS Z-score | 1.023 | 0.852 |
Model quality | ||
Ramachandran plot normality | -1.102 50 | -1.321 44 |
Rotamer normality | -0.784 81 | -1.527 67 |
Coarse packing | -0.030 60 | -0.175 53 |
Fine packing | -1.514 31 | -1.434 34 |
Bump severity | 0.007 67 | 0.021 38 |
Hydrogen bond satisfaction | 0.865 19 | 0.894 43 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 9 |
Side chains flipped | 0 |
Waters removed | 64 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 19 |