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Crystal structure of HLA-A*11:01 in complex with SVLNDILSRL, an 10-mer epitope from SARS-CoV-2 Spike (S975-984)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7S8Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 25% PEG3350, 0.2M NaCl and 0.1M Tris HCl pH8.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.85 α = 90 b = 84.85 β = 90 c = 311.296 γ = 120
Symmetry Space Group P 31 2 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 EIGER X 16M 2022-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953732 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 3.32 47.5 99.6 0.215 0.248 0.119 0.989 5.9 4.1 20087 71.74
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 3.32 3.59 99.5 0.877 1.014 0.495 0.553 1.6 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.32 47.5 1.34 20022 971 99.5 0.2228 0.2212 0.2215 0.2514 0.252 71.67
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.5105 f_angle_d 0.4087 f_chiral_restr 0.0383 f_plane_restr 0.0033 f_bond_d 0.0013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9451 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 11
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing