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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z54571979 |
This entry was created with PDB-REDO version 7.34. |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 112.560 Å | b: 52.810 Å | c: 44.620 Å | α: 90.00° | β: 103.20° | γ: 90.00° |
Resolution | 1.87 Å | Reflections | 21169 | Test set | 1077 (5.1%) | ||
R | 0.1860 | R-free | 0.2510 | ||||
According to PDB-REDO | |||||||
Resolution | 1.87 Å | Reflections | 21169 | Test set | 1077 (5.1%) | 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 | 0.1956 | 0.2143 |
R-free | 0.2568 | 0.2614 |
Bond length RMS Z-score | 0.686 | 0.342 |
Bond angle RMS Z-score | 1.044 | 0.612 |
Model quality | ||
Ramachandran plot normality | -1.724 35 | -1.678 36 |
Rotamer normality | -1.849 61 | -0.125 91 |
Coarse packing | -0.372 42 | -0.486 37 |
Fine packing | -1.627 26 | -1.384 37 |
Bump severity | 0.003 82 | 0.002 87 |
Hydrogen bond satisfaction | 0.891 39 | 0.897 46 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 6 |
Side chains flipped | 0 |
Waters removed | 53 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |