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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1129283193 |
This entry was created with PDB-REDO version 7.34. |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 111.643 Å | b: 52.352 Å | c: 44.369 Å | α: 90.00° | β: 103.08° | γ: 90.00° |
Resolution | 1.88 Å | Reflections | 20087 | Test set | 1030 (5.1%) | ||
R | 0.1990 | R-free | 0.2660 | ||||
According to PDB-REDO | |||||||
Resolution | 1.88 Å | Reflections | 20087 | Test set | 1030 (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 | 0.2072 | 0.2190 |
R-free | 0.2700 | 0.2770 |
Bond length RMS Z-score | 0.655 | 0.345 |
Bond angle RMS Z-score | 1.035 | 0.620 |
Model quality | ||
Ramachandran plot normality | -2.884 17 | -2.387 23 |
Rotamer normality | -2.053 57 | -1.038 77 |
Coarse packing | -0.178 52 | -0.247 49 |
Fine packing | -1.614 27 | -1.331 39 |
Bump severity | 0.014 49 | 0.010 58 |
Hydrogen bond satisfaction | 0.885 33 | 0.882 30 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 9 |
Side chains flipped | 0 |
Waters removed | 66 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |