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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease in complex with PCM-0102269 |
This entry was created with PDB-REDO version 7.36. |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 112.889 Å | b: 53.003 Å | c: 44.457 Å | α: 90.00° | β: 103.04° | γ: 90.00° |
Resolution | 1.68 Å | Reflections | 29092 | Test set | 1441 (5.0%) | ||
R | 0.1820 | R-free | 0.2220 | ||||
According to PDB-REDO | |||||||
Resolution | 1.68 Å | Reflections | 29092 | Test set | 1441 (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 | 0.1899 | 0.1963 |
R-free | 0.2262 | 0.2306 |
Bond length RMS Z-score | 0.667 | 0.413 |
Bond angle RMS Z-score | 1.019 | 0.688 |
Model quality | ||
Ramachandran plot normality | -1.641 37 | -1.122 50 |
Rotamer normality | -0.965 78 | -0.550 85 |
Coarse packing | -0.284 47 | -0.262 48 |
Fine packing | -1.551 29 | -1.354 38 |
Bump severity | 0.020 39 | 0.011 56 |
Hydrogen bond satisfaction | 0.882 30 | 0.866 19 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 8 |
Side chains flipped | 0 |
Waters removed | 62 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 0 |
Residues fitting density worse | 0 |