9ART
Crystal structure of SARS-CoV-2 main protease A191T mutant in complex with an inhibitor 5h
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 8UH9 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 298 | 0.1 M HEPES pH 7.5, 12 % w/v Polyethylene glycol 3,350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.05 | 40.04 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 45.111 | ¦Á = 114.79 |
b = 53.54 | ¦Â = 97.99 |
c = 63.86 | ¦Ã = 89.99 |
Symmetry | |
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Space Group | P 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 EIGER X 4M | 2023-11-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS-II BEAMLINE 19-ID | 0.979497 | NSLS-II | 19-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 1.49 | 57.3 | 92.7 | 0.985 | 6.58 | 6.58 | 84234 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.49 | 1.51 | 0.453 |
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 | 1.49 | 57.3 | 80067 | 4166 | 96.22 | 0.19803 | 0.19624 | 0.23148 | RANDOM | 29.622 |
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] | |
-0.5 | -0.34 | -0.5 | 0.31 | 0.02 | 0.22 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 12.754 |
r_dihedral_angle_2_deg | 10.304 |
r_dihedral_angle_1_deg | 7.345 |
r_long_range_B_refined | 6.537 |
r_long_range_B_other | 6.518 |
r_scangle_other | 4.99 |
r_mcangle_it | 3.255 |
r_mcangle_other | 3.254 |
r_scbond_it | 3.205 |
r_scbond_other | 3.205 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4720 |
Nucleic Acid Atoms | |
Solvent Atoms | 291 |
Heterogen Atoms | 82 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |
DIALS | data scaling |
MOLREP | phasing |