9EOX
SARS-CoV2 major protease in covalent complex with a soluble inhibitor.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7PFL |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 18% w/v PEG3350 0.2M potassium-thiocyanate 0.1M bis-tris propane pH 8.7 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.67 | 53.92 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 69.463 | α = 79.5 |
b = 85.052 | β = 87.62 |
c = 93.897 | γ = 84.14 |
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 EIGER2 X 16M | 2021-10-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.979499 | Diamond | I04 |
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 | 2.54 | 46.39 | 60 | 0.187 | 0.22 | 0.115 | 0.977 | 4.6 | 3.6 | 41800 |
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 | 2.54 | 2.76 | 13.5 | 0.628 | 0.734 | 0.379 | 0.635 | 1.4 | 3.7 |
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 | 2.54 | 46.39 | 39749 | 2051 | 59.99 | 0.19073 | 0.18863 | 0.23127 | RANDOM | 33.16 |
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] | |
-0.22 | 0.07 | -0.1 | 0.22 | -0.04 | -0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 25.832 |
r_dihedral_angle_3_deg | 16.679 |
r_long_range_B_refined | 8.392 |
r_long_range_B_other | 8.392 |
r_dihedral_angle_1_deg | 6.769 |
r_scangle_other | 4.914 |
r_mcangle_it | 4.076 |
r_mcangle_other | 4.076 |
r_scbond_it | 3.007 |
r_scbond_other | 3.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 14298 |
Nucleic Acid Atoms | |
Solvent Atoms | 171 |
Heterogen Atoms | 137 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
STARANISO | data scaling |
XDS | data reduction |
PHASER | phasing |