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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z33545544 |
This entry was created with PDB-REDO version 8.07. |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 112.530 Å | b: 52.810 Å | c: 52.810 Å | α: 90.00° | β: 102.15° | γ: 90.00° |
Resolution | 2.07 Å | Reflections | 15700 | Test set | 793 (5.1%) | ||
R | 0.1811 | R-free | 0.2649 | ||||
According to PDB-REDO | |||||||
Resolution | 2.07 Å | Reflections | 15700 | Test set | 793 (5.1%) | ||
Twin | false | Radiation damage | 20 | ||||
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 | 0.1895 | 0.2101 |
R-free | 0.2684 | 0.2678 |
Bond length RMS Z-score | 1.390 | 0.255 |
Bond angle RMS Z-score | 1.005 | 0.501 |
Model quality | ||
Ramachandran plot normality | -2.676 21 | -1.967 32 |
Rotamer normality | -2.334 44 | -1.036 71 |
Coarse packing | 0.402 67 | 0.291 62 |
Fine packing | -1.532 30 | -1.379 37 |
Bump severity | 0.007 65 | 0.010 56 |
Hydrogen bond satisfaction | 0.886 34 | 0.894 42 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 9 |
Side chains flipped | 0 |
Waters removed | 108 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |