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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z24758179 |
This entry was created with PDB-REDO version 7.34. |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 112.514 Å | b: 52.708 Å | c: 44.455 Å | α: 90.00° | β: 103.04° | γ: 90.00° |
Resolution | 1.61 Å | Reflections | 31983 | Test set | 1584 (5.0%) | ||
R | 0.1980 | R-free | 0.2460 | ||||
According to PDB-REDO | |||||||
Resolution | 1.61 Å | Reflections | 31983 | Test set | 1584 (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 | 0.2121 | 0.2062 |
R-free | 0.2578 | 0.2568 |
Bond length RMS Z-score | 0.681 | 0.595 |
Bond angle RMS Z-score | 1.001 | 0.777 |
Model quality | ||
Ramachandran plot normality | -2.006 29 | -1.837 33 |
Rotamer normality | -1.483 68 | -0.886 79 |
Coarse packing | -0.363 43 | -0.395 41 |
Fine packing | -1.454 34 | -1.474 33 |
Bump severity | 0.004 78 | 0.019 41 |
Hydrogen bond satisfaction | 0.878 27 | 0.891 39 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 8 |
Side chains flipped | 0 |
Waters removed | 64 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 2 |
Residues fitting density worse | 0 |