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Crystal structure of a TCR in complex with HLA-A*11:01 bound to KRAS peptide (VVVGAGGVGK)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HN7 2HN7, 6BJ2, 2F53 experimental model PDB 6BJ2 2HN7, 6BJ2, 2F53 experimental model PDB 2F53 2HN7, 6BJ2, 2F53
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Ammonium citrate tribasic pH 7.0, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.36 63.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.552 α = 90 b = 145.552 β = 90 c = 120.599 γ = 90
Symmetry Space Group P 41 2 2
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 XE 16M 2020-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 2.58 65.09 100 0.151 0.153 0.03 0.999 14.7 26.7 41420
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 2.58 2.62 100 5.709 5.816 1.102 0.343 0.3 27.6
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 2HN7, 6BJ2, 2F53 2.58 65.09 39259 2127 99.99 0.2094 0.20595 0.2159 0.27356 0.275 RANDOM 88.001
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] -0.35 -0.35 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.807 r_dihedral_angle_3_deg 20.306 r_dihedral_angle_4_deg 18.843 r_dihedral_angle_1_deg 8.746 r_long_range_B_refined 6.445 r_long_range_B_other 6.445 r_scangle_other 4.484 r_mcangle_it 4.382 r_mcangle_other 4.381 r_scbond_it 3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.807 r_dihedral_angle_3_deg 20.306 r_dihedral_angle_4_deg 18.843 r_dihedral_angle_1_deg 8.746 r_long_range_B_refined 6.445 r_long_range_B_other 6.445 r_scangle_other 4.484 r_mcangle_it 4.382 r_mcangle_other 4.381 r_scbond_it 3 r_scbond_other 2.783 r_mcbond_it 2.775 r_mcbond_other 2.773 r_angle_refined_deg 1.767 r_angle_other_deg 1.227 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 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 6592 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing