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Crystal Structure of Heterotrimeric Anti-TIGIT Fabs in complex with human TIGIT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NM4 Fab constant domain, chain H and L experimental model PDB 6B3S Variable domain, HCDR3 removed, chain H and L of BMS-986207 experimental model PDB 1PLG CHA.9.543 variable domain, chain H and L experimental model PDB 3UDW TIGIT, chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 300 0.2 M sodium phosphate monobasic monohydrate, 20% w/v Polyethylene glycol 1,000
Crystal Properties Matthews coefficient Solvent content 2.45 49.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.85 α = 90 b = 216.91 β = 95.97 c = 109.45 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 PILATUS 6M 2020-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1 APS 17-ID
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 2.306 108.856 70.2 0.14 0.168 0.091 0.985 7.5 3.3 65410 35.04
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 2.306 2.479 0.694 0.854 0.491 0.6 1.5
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 2.31 45.6 1.36 65378 3191 70.18 0.229 0.227 0.2231 0.2686 0.2645 34.66
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 16.0905 f_angle_d 0.8813 f_chiral_restr 0.1008 f_plane_restr 0.0144 f_bond_d 0.0049
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14751 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 28
Software Software Software Name Purpose PHENIX refinement STARANISO data scaling XSCALE data scaling Coot model building autoPROC data reduction PHASER phasing