7SIS
SARS-CoV-2 Spike-derived peptide S976-984 (VLNDILSRL) presented by HLA-A*02:01
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 293 | 20% PEG 3350, 0.2M Ammonium Formate, 1 mM CdCl2 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.01 | 59.07 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 60.336 | α = 90 |
b = 80.753 | β = 90 |
c = 110.709 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 16M | 2020-07-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.954 | Australian Synchrotron | MX2 |
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 | 1.9 | 48.33 | 99.3 | 0.108 | 0.115 | 0.039 | 0.997 | 11.7 | 8.5 | 42888 | 32.58 |
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 | 1.9 | 1.95 | 90.5 | 1.276 | 1.358 | 0.457 | 0.595 | 8.3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | 1OGA | 1.9 | 45.66 | 42825 | 2191 | 99.4 | 0.173 | 0.171 | 0.206 | RANDOM | 37.09 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-1.502 | 1.4674 | 0.0346 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 17.25 |
t_omega_torsion | 3.65 |
t_angle_deg | 1 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_trig_c_planes | |
t_gen_planes | |
t_it | |
t_nbd | |
t_improper_torsion |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3161 |
Nucleic Acid Atoms | |
Solvent Atoms | 356 |
Heterogen Atoms | 6 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |