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Gag:02 TCR in complex with HLA-E featuring a non-natural amino acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NDQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 22.3% (w/v) PEG 1500, 89 mM MMT pH 9.0
Crystal Properties Matthews coefficient Solvent content 3.13 60.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.98 α = 90 b = 88.98 β = 90 c = 293.57 γ = 90
Symmetry Space Group P 43 21 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 2020-12-03 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) 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 2.9 61.597 99.9 0.23 0.082 0.998 8.6 8.8 27166
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.95 99.2 2.569 0.933 0.458 1 8.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7NDQ 2.9 61.597 27136 1336 99.823 0.245 0.2419 0.2449 0.3015 0.3035 68.718
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] 1.801 1.801 -3.602
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.574 r_dihedral_angle_4_deg 19.529 r_dihedral_angle_3_deg 19.164 r_dihedral_angle_1_deg 8.752 r_angle_refined_deg 1.588 r_angle_other_deg 1.135 r_symmetry_nbd_refined 0.225 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.187 r_nbd_other 0.187
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.574 r_dihedral_angle_4_deg 19.529 r_dihedral_angle_3_deg 19.164 r_dihedral_angle_1_deg 8.752 r_angle_refined_deg 1.588 r_angle_other_deg 1.135 r_symmetry_nbd_refined 0.225 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.187 r_nbd_other 0.187 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.173 r_symmetry_xyhbond_nbd_other 0.096 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.058 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6529 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction DIALS data scaling PHASER phasing