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Emergence of immune escape at dominant SARS-CoV-2 killer T-cell epitope
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7P3D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 0.2 M ammonium sulphate, 0.1 M Tris, pH 8.5, and 25 % w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.56 51.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 229.24 α = 90 b = 46.45 β = 96.75 c = 184.72 γ = 90
Symmetry Space Group C 1 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 PILATUS 6M 2021-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91808 Diamond I04-1
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 2.68 113.83 99.5 0.133 0.155 0.078 0.998 6.3 3.9 55107
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 2.68 2.75 99.8 3.489 4.031 1.997 0.441 4
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 7P3D 3 113.83 37569 1931 99.33 0.2314 0.2281 0.2285 0.2957 0.2911 RANDOM 104.77
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] -7.05 -0.93 4.95 2.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.493 r_dihedral_angle_3_deg 19.277 r_dihedral_angle_4_deg 17.093 r_dihedral_angle_1_deg 9.39 r_angle_refined_deg 1.097 r_angle_other_deg 1.039 r_chiral_restr 0.032 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_gen_planes_other 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.493 r_dihedral_angle_3_deg 19.277 r_dihedral_angle_4_deg 17.093 r_dihedral_angle_1_deg 9.39 r_angle_refined_deg 1.097 r_angle_other_deg 1.039 r_chiral_restr 0.032 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13364 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing PDB_EXTRACT data extraction DIALS data scaling