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Crystal Structure of HLA-A*0201 in complex with SARS-CoV-2 N316-324
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GSO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 20% 3350, 0.2M NaFluoride, 1 mM CdCl2
Crystal Properties Matthews coefficient Solvent content 2.98 58.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.192 α = 90 b = 79.546 β = 90 c = 111.578 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 2020-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95372 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 1.396 48 99.4 0.064 0.066 0.018 0.999 19.3 13.4 106332 20.99
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 1.4 1.42 88.4 1.349 1.405 0.385 0.697 12.6
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 3GSO 1.396 48 106241 5319 99.4 0.1948 0.1943 0.1925 0.2035 0.2053 random 24.42
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] 2.8527 -1.9308 -0.9219
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.84 t_omega_torsion 4.13 t_angle_deg 0.94 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 15.84 t_omega_torsion 4.13 t_angle_deg 0.94 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 3152 Nucleic Acid Atoms Solvent Atoms 476 Heterogen Atoms 10
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing BUSTER refinement PDB_EXTRACT data extraction