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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102739 |
This entry was created with PDB-REDO version 7.34. |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 112.861 Å | b: 52.958 Å | c: 44.518 Å | α: 90.00° | β: 103.22° | γ: 90.00° |
Resolution | 1.70 Å | Reflections | 27915 | Test set | 1387 (5.0%) | ||
R | 0.1870 | R-free | 0.2330 | ||||
According to PDB-REDO | |||||||
Resolution | 1.70 Å | Reflections | 27915 | Test set | 1387 (5.0%) | ||
Twin | false | Radiation damage | N/A | ||||
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 | 0.1976 | 0.1990 |
R-free | 0.2370 | 0.2355 |
Bond length RMS Z-score | 0.714 | 0.415 |
Bond angle RMS Z-score | 1.074 | 0.693 |
Model quality | ||
Ramachandran plot normality | -1.843 33 | -1.494 40 |
Rotamer normality | -1.454 69 | -0.688 83 |
Coarse packing | -0.289 47 | -0.277 47 |
Fine packing | -1.709 23 | -1.594 28 |
Bump severity | 0.008 64 | 0.005 74 |
Hydrogen bond satisfaction | 0.879 28 | 0.894 43 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 9 |
Side chains flipped | 0 |
Waters removed | 32 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 1 |
Residues fitting density worse | 0 |