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UL40:01 TCR in complex with HLA-E with a non-natural amino acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ESV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 12% (w/v) PEG 8000, 55 mM MOPS pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.02 59.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.614 α = 90 b = 76.577 β = 107.639 c = 130.341 γ = 90
Symmetry Space Group P 1 21 1
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 2020-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97951 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 2.999 65.27 99.9 0.101 0.064 0.995 13.4 3.4 44666
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 2.999 3.05 2.198 1.425 0.134
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 2ESV 2.999 65.27 44652 2205 99.904 0.224 0.2212 0.2348 0.2694 0.2872 68.634
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] -1.311 -0.27 1.668 -0.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.368 r_dihedral_angle_3_deg 18.177 r_dihedral_angle_4_deg 15.18 r_dihedral_angle_1_deg 7.638 r_angle_refined_deg 1.286 r_angle_other_deg 1.064 r_nbd_refined 0.194 r_symmetry_nbd_other 0.174 r_nbtor_refined 0.162 r_nbd_other 0.157
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.368 r_dihedral_angle_3_deg 18.177 r_dihedral_angle_4_deg 15.18 r_dihedral_angle_1_deg 7.638 r_angle_refined_deg 1.286 r_angle_other_deg 1.064 r_nbd_refined 0.194 r_symmetry_nbd_other 0.174 r_nbtor_refined 0.162 r_nbd_other 0.157 r_symmetry_xyhbond_nbd_refined 0.153 r_ncsr_local_group_3 0.143 r_symmetry_nbd_refined 0.142 r_xyhbond_nbd_refined 0.141 r_ncsr_local_group_4 0.137 r_symmetry_xyhbond_nbd_other 0.136 r_ncsr_local_group_2 0.135 r_ncsr_local_group_1 0.119 r_symmetry_nbtor_other 0.069 r_dihedral_angle_other_3_deg 0.051 r_chiral_restr 0.045 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13021 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing