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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z979145504 |
This entry was created with PDB-REDO version 8.07. |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 112.577 Å | b: 52.959 Å | c: 52.959 Å | α: 90.00° | β: 102.99° | γ: 90.00° |
Resolution | 1.40 Å | Reflections | 46629 | Test set | 2260 (4.8%) | ||
R | 0.1795 | R-free | 0.2128 | ||||
According to PDB-REDO | |||||||
Resolution | 1.40 Å | Reflections | 46629 | Test set | 2260 (4.8%) | ||
Twin | false | Radiation damage | 14 | ||||
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 | 0.1851 | 0.1856 |
R-free | 0.2177 | 0.2174 |
Bond length RMS Z-score | 1.305 | 0.261 |
Bond angle RMS Z-score | 1.017 | 0.535 |
Model quality | ||
Ramachandran plot normality | -0.323 75 | -0.337 74 |
Rotamer normality | -0.303 85 | 0.518 95 |
Coarse packing | 0.511 71 | 0.435 68 |
Fine packing | -1.635 26 | -1.492 32 |
Bump severity | 0.005 72 | 0.009 59 |
Hydrogen bond satisfaction | 0.902 53 | 0.886 34 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 8 |
Side chains flipped | 0 |
Waters removed | 40 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 2 |
Residues fitting density worse | 0 |