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Novel Anti-Mesothelin Antibodies Enable Crystallography of the Intact Mesothelin Ectodo- main and Engineering of Potent, T cell-engaging Bispecific Therapeutics
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4F3F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 295 Tris (8.0), sodium citrate, Peg3350
Crystal Properties Matthews coefficient Solvent content 3.68 66.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.112 α = 90 b = 124.862 β = 90 c = 302.748 γ = 90
Symmetry Space Group I 2 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 PILATUS 6M 2019-08-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.97926 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.35 50 98.7 0.149 0.164 0.068 8.4 5.8 17506
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 3.35 3.41 96.1 0.934 1.035 0.438 0.598 5.6
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 4F3F 3.38 44.38 16652 851 97.88 0.2315 0.2296 0.2269 0.2676 0.2639 RANDOM 118.853
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] 14.26 -6.74 -7.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.672 r_dihedral_angle_4_deg 26.63 r_dihedral_angle_3_deg 19.068 r_dihedral_angle_1_deg 8.609 r_angle_refined_deg 1.14 r_angle_other_deg 1.093 r_chiral_restr 0.032 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.672 r_dihedral_angle_4_deg 26.63 r_dihedral_angle_3_deg 19.068 r_dihedral_angle_1_deg 8.609 r_angle_refined_deg 1.14 r_angle_other_deg 1.093 r_chiral_restr 0.032 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5216 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 28
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing