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Structural Elucidation of the Mesothelin Mucin16 CA125 Interaction
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8CXC experimental model PDB 7SA9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 Bis-Tris, NH4CL, PEG3350
Crystal Properties Matthews coefficient Solvent content 3.65 66.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.203 α = 90 b = 73.237 β = 90 c = 75.054 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 6M 2023-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.00 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) 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 2.65 50 99 0.066 0.074 0.034 0.992 20.9 5.3 9868
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 2.65 2.7 100 0.628 0.691 0.283 0.822 5.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.65 33.42 9117 480 98.25 0.25049 0.24781 0.2455 0.29849 0.2933 RANDOM 80.658
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] -1.5 1.17 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.779 r_dihedral_angle_4_deg 21.719 r_dihedral_angle_3_deg 17.762 r_long_range_B_other 7.324 r_long_range_B_refined 7.323 r_dihedral_angle_1_deg 7.057 r_scangle_other 6.297 r_mcangle_it 4.553 r_mcangle_other 4.552 r_scbond_it 4.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.779 r_dihedral_angle_4_deg 21.719 r_dihedral_angle_3_deg 17.762 r_long_range_B_other 7.324 r_long_range_B_refined 7.323 r_dihedral_angle_1_deg 7.057 r_scangle_other 6.297 r_mcangle_it 4.553 r_mcangle_other 4.552 r_scbond_it 4.154 r_scbond_other 4.153 r_mcbond_it 3.116 r_mcbond_other 3.102 r_angle_refined_deg 1.551 r_angle_other_deg 1.148 r_chiral_restr 0.059 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1469 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling DENZO data reduction PHASER phasing