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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 6DFX experimental model PDB 4ONH experimental model PDB 7LGD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.1 M ammonium citrate dibasic, and 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.55 51.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.105 α = 90 b = 102.725 β = 90 c = 160.147 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 2.04 48.9 99.97 0.999 16.2 10.7 61913
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 2.04 2.11 0.782
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 2.04 48.9 58820 3093 99.9 0.18967 0.18745 0.1971 0.23157 0.2361 RANDOM 32.044
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] 1.14 0.34 -1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.205 r_dihedral_angle_4_deg 21.114 r_dihedral_angle_3_deg 16.596 r_long_range_B_refined 8.269 r_long_range_B_other 8.032 r_dihedral_angle_1_deg 7.082 r_scangle_other 5.628 r_mcangle_it 4.041 r_mcangle_other 4.04 r_scbond_it 3.607
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.205 r_dihedral_angle_4_deg 21.114 r_dihedral_angle_3_deg 16.596 r_long_range_B_refined 8.269 r_long_range_B_other 8.032 r_dihedral_angle_1_deg 7.082 r_scangle_other 5.628 r_mcangle_it 4.041 r_mcangle_other 4.04 r_scbond_it 3.607 r_scbond_other 3.606 r_mcbond_it 2.797 r_mcbond_other 2.797 r_angle_refined_deg 1.766 r_angle_other_deg 0.866 r_chiral_restr 0.115 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6586 Nucleic Acid Atoms Solvent Atoms 722 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing