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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z3241250482 |
This entry was created with PDB-REDO version 7.34. |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 112.225 Å | b: 52.701 Å | c: 44.634 Å | α: 90.00° | β: 102.89° | γ: 90.00° |
Resolution | 1.74 Å | Reflections | 26161 | Test set | 1302 (5.0%) | ||
R | 0.1780 | R-free | 0.2310 | ||||
According to PDB-REDO | |||||||
Resolution | 1.74 Å | Reflections | 26161 | Test set | 1302 (5.0%) | 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 | 0.1869 | 0.1901 |
R-free | 0.2372 | 0.2384 |
Bond length RMS Z-score | 0.656 | 0.549 |
Bond angle RMS Z-score | 1.023 | 0.753 |
Model quality | ||
Ramachandran plot normality | -1.613 37 | -1.384 43 |
Rotamer normality | -0.997 77 | 0.055 93 |
Coarse packing | -0.237 49 | -0.268 48 |
Fine packing | -1.584 28 | -1.399 36 |
Bump severity | 0.003 82 | 0.005 74 |
Hydrogen bond satisfaction | 0.900 50 | 0.900 50 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 9 |
Side chains flipped | 0 |
Waters removed | 62 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 1 |
Residues fitting density worse | 0 |