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Crystal Structure of HLA-A*11:01 in complex with NSASFSTFK, an 9-mer epitope from SARS-CoV-2 spike (S370-378)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WJN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 2M Ammonium Sulfate, 0.1M Calcium cacodylate pH 6.5, 0.2M sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.34 47.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.873 α = 90 b = 38.451 β = 94.63 c = 110.059 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS 12M 2020-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.98 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.5 46.72 100 0.071 0.999 13.8 6.8 67146 20.44
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 100 1.058 0.754 7
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 5WJN 1.5 38.41 67130 3406 100 0.1894 0.1879 0.1864 0.2186 0.2196 RANDOM 24.56
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] -8.7172 4.0711 5.0657 3.6515
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.59 t_omega_torsion 3.97 t_angle_deg 0.95 t_bond_d 0.008 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 14.59 t_omega_torsion 3.97 t_angle_deg 0.95 t_bond_d 0.008 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 3160 Nucleic Acid Atoms Solvent Atoms 447 Heterogen Atoms 21
Software Software Software Name Purpose BUSTER refinement Aimless data scaling PDB_EXTRACT data extraction Coot model building