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HPV_Jin TCR in complex with HLA-A*02:01 presenting HPV16 E7 9mer peptide (11-YMLDLQPET-19)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XQP TCR experimental model PDB 6VRN pHLA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 22% PEG 3350, 0.2 M sodium sulfate, 0.1 M Bis-tris propane pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.02 α = 90 b = 203.81 β = 90 c = 206.22 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 9M 2023-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.95370 CLSI 08ID-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 3.13 113.02 100 0.21 0.243 0.121 0.994 9.4 7.5 84686
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 3.13 3.21 100 1.398 1.623 0.817 0.589 1.7 7.5
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 3.13 102.11 80370 4235 99.97 0.22641 0.22423 0.2251 0.26741 0.2641 RANDOM 74.835
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] -5.1 4.13 0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.648 r_dihedral_angle_1_deg 6.018 r_long_range_B_refined 4.208 r_long_range_B_other 4.208 r_dihedral_angle_2_deg 3.101 r_mcangle_it 2.594 r_mcangle_other 2.594 r_scangle_other 2.122 r_mcbond_it 1.436 r_mcbond_other 1.436
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.648 r_dihedral_angle_1_deg 6.018 r_long_range_B_refined 4.208 r_long_range_B_other 4.208 r_dihedral_angle_2_deg 3.101 r_mcangle_it 2.594 r_mcangle_other 2.594 r_scangle_other 2.122 r_mcbond_it 1.436 r_mcbond_other 1.436 r_scbond_it 1.152 r_scbond_other 1.152 r_angle_refined_deg 0.739 r_angle_other_deg 0.31 r_chiral_restr 0.038 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 25093 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 146
Software Software Software Name Purpose REFMAC refinement xia2 data scaling PHASER phasing PDB_EXTRACT data extraction xia2 data reduction