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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with Z1271660837 |
This entry was created with PDB-REDO version 8.07. |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 112.489 Å | b: 52.630 Å | c: 52.630 Å | α: 90.00° | β: 102.98° | γ: 90.00° |
Resolution | 1.48 Å | Reflections | 40538 | Test set | 2001 (4.9%) | ||
R | 0.1833 | R-free | 0.2235 | ||||
According to PDB-REDO | |||||||
Resolution | 1.48 Å | Reflections | 40538 | Test set | 2001 (4.9%) | ||
Twin | false | Radiation damage | 36 | ||||
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 | 0.1907 | 0.1940 |
R-free | 0.2307 | 0.2317 |
Bond length RMS Z-score | 1.292 | 0.583 |
Bond angle RMS Z-score | 0.989 | 0.697 |
Model quality | ||
Ramachandran plot normality | -0.924 58 | -0.833 60 |
Rotamer normality | -0.254 86 | 0.141 91 |
Coarse packing | 0.532 71 | 0.490 70 |
Fine packing | -1.507 31 | -1.448 34 |
Bump severity | 0.005 72 | 0.009 59 |
Hydrogen bond satisfaction | 0.901 51 | 0.911 65 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 6 |
Side chains flipped | 0 |
Waters removed | 50 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |