8TPB
Synthesis, X-Ray Crystallographic and Biological Activities of Covalent, Non-Peptidic Inhibitors of SARS-CoV-2 Main Protease
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 295.15 | 25% PEG 3350, 0.1M Hepes PH 7.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.01 | 38.82 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 44.857 | α = 90 |
b = 53.597 | β = 100.21 |
c = 114.959 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315r | 2022-07-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-BM | 0.97919 | APS | 19-BM |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | |||||
1 | 1.63 | 50 | 79.4 | 0.109 | 0.123 | 0.057 | 1 | 5.4 | 4.2 | 52904 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.69 | 1.72 | 24.6 | 4.457 | 5.739 | 3.553 | 0.055 | 1.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.88 | 43.842 | 1.33 | 43299 | 1632 | 98.43 | 0.1999 | 0.198 | 0.2476 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 6.643 |
f_angle_d | 1.055 |
f_chiral_restr | 0.06 |
f_bond_d | 0.008 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4754 |
Nucleic Acid Atoms | |
Solvent Atoms | 315 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
HKL-3000 | data scaling |
HKL-3000 | data reduction |
PHASER | phasing |