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Miniaturized HLA A*02-TAX bound to A6c134 TCR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GRM in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 50 mM magnesium formate, 17% PEG 3350 microseeded
Crystal Properties Matthews coefficient Solvent content 3.82 67.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.906 α = 90 b = 106.906 β = 90 c = 190.592 γ = 120
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 2024-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.9202 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3.4 46.62 99.25 0.2782 0.3274 0.1707 0.976 4.33 3.5 33320 107.63
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.4 3.52 99.29 2.599 3.046 1.576 0.149 0.64 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.4 46.62 1.96 33280 1377 99.26 0.2204 0.2182 0.2187 0.269 0.2692 125.44
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.7525 f_angle_d 0.4624 f_chiral_restr 0.0393 f_plane_restr 0.0038 f_bond_d 0.0019
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10866 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 94
Software Software Software Name Purpose PHENIX refinement XDS data reduction PHASER phasing XDS data scaling Aimless data reduction