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SARS-CoV-2 Spike-derived peptide S417-425 K417T mutant (TIADYNYKL) presented by HLA-A*02:01
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OGA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 14% P3350; 0.1M NaFlu; 2% EG; 1 mM CdCl2
Crystal Properties Matthews coefficient Solvent content 2.44 49.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.171 α = 90 b = 79.105 β = 90 c = 110.86 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment 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 2021-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953659 Australian Synchrotron MX2
Data Collection Overall 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 47.89 100 0.067 0.072 0.026 0.999 15.7 7.5 66786 26.89
Highest Resolution Shell 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 1.63 1.66 100 1.22 1.313 0.479 0.668 7.3
Refinement Statistics 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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1OGA 1.63 23.81 66688 3347 100 0.18 0.179 0.1855 0.195 0.2048 RANDOM 30.37
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] 5.0733 -2.3207 -2.7526
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.39 t_omega_torsion 3.78 t_angle_deg 1.01 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.39 t_omega_torsion 3.78 t_angle_deg 1.01 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3169 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms 3
Software Software Software Name Purpose BUSTER refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction