8FTL
Crystal structure of the SARS-CoV-2 (COVID-19) main protease (Mpro) in complex with inhibitor Jun89-3-C1
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293.15 | 25% PEG 3350, 0.1M Potassium/Sodium Tartrate, 0.005M Magnesium Chloride |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.01 | 38.79 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 45.365 | ¦Á = 90 |
b = 53.725 | ¦Â = 101.38 |
c = 113.799 | ¦Ã = 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 | PIXEL | DECTRIS PILATUS3 6M | 2022-07-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 1.0 | APS | 19-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.08 | 50 | 98.3 | 0.074 | 21.39 | 3.9 | 32051 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.08 | 2.12 | 99.2 | 0.493 | 2.2 | 3.8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.08 | 48.45 | 30435 | 1606 | 98.19 | 0.20606 | 0.20325 | 0.25867 | RANDOM | 49.946 |
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] | |
2.38 | 1.24 | -3.36 | 0.45 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.95 |
r_dihedral_angle_4_deg | 19.714 |
r_dihedral_angle_3_deg | 15.437 |
r_long_range_B_refined | 7.231 |
r_long_range_B_other | 7.224 |
r_dihedral_angle_1_deg | 6.966 |
r_scangle_other | 4.947 |
r_scbond_it | 3.615 |
r_scbond_other | 3.615 |
r_mcangle_it | 3.558 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4696 |
Nucleic Acid Atoms | |
Solvent Atoms | 116 |
Heterogen Atoms | 70 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
PDB_EXTRACT | data extraction |
HKL-2000 | data scaling |
PHASER | phasing |