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Structure of SARS coronavirus main protease in complex with the alpha-ketoamide (S)-N-benzyl-3-((S)-2-cinnamamido-3-phenylpropanamido)-2-oxo-4-((S)-2-oxopyrrolidin-3-yl)butanamide |
This entry was created with PDB-REDO version 7.14. |
From original header | |||||||
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Spacegroup | C 1 2 1 | a: 108.196 Å | b: 82.284 Å | c: 53.435 Å | α: 90.00° | β: 103.95° | γ: 90.00° |
Resolution | 1.62 Å | Reflections | 56524 | Test set | 2869 (5.1%) | ||
R | 0.1720 | R-free | 0.2000 | ||||
According to PDB-REDO | |||||||
Resolution | 1.62 Å | Reflections | 56524 | Test set | 2869 (5.1%) | ||
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 | 0.1725 | 0.1425 |
R-free | 0.1999 | 0.1796 |
Bond length RMS Z-score | 1.307 | 0.643 |
Bond angle RMS Z-score | 1.245 | 0.776 |
Model quality | ||
Ramachandran plot normality | -0.640 64 | -0.123 77 |
Rotamer normality | -1.280 72 | 0.094 93 |
Coarse packing | -0.731 26 | -0.579 32 |
Fine packing | -1.701 24 | -1.505 31 |
Bump severity | 0.016 45 | 0.025 34 |
Hydrogen bond satisfaction | 0.883 31 | 0.871 22 |
WHAT_CHECK | Report | Report |
Kleywegt-like plot |
Description | Count |
---|---|
Rotamers changed | 5 |
Side chains flipped | 0 |
Waters removed | 93 |
Peptides flipped | 0 |
Chiralities fixed | 0 |
Residues fitting density better | 150 |
Residues fitting density worse | 2 |