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Structural basis for recognition of SARS-CoV-2 conserved nucleocapside epitopes by dominant T cell receptors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3REV experimental model PDB 8CX4 experimental model PDB 7LGD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 0.1M Tris-base/hydrochloric acid (pH 7.0), 0.2 M lithium sulfate, and 1.9 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.92 57.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.978 α = 90 b = 93.303 β = 90 c = 261.912 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 EIGER2 S 9M 2024-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.9792 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.95 76.1 99.9 0.995 10.9 7.5 48369
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.95 3.06 0.687
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.95 76.1 45924 2450 99.97 0.19581 0.19354 0.1944 0.23786 0.2384 RANDOM 44.418
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] -0.28 3.31 -3.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.041 r_long_range_B_refined 14.102 r_dihedral_angle_2_deg 12.331 r_mcangle_it 7.819 r_dihedral_angle_1_deg 7.104 r_scbond_it 6.749 r_mcbond_it 4.999 r_angle_refined_deg 1.94 r_chiral_restr 0.122 r_bond_refined_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.041 r_long_range_B_refined 14.102 r_dihedral_angle_2_deg 12.331 r_mcangle_it 7.819 r_dihedral_angle_1_deg 7.104 r_scbond_it 6.749 r_mcbond_it 4.999 r_angle_refined_deg 1.94 r_chiral_restr 0.122 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13246 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing