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Crystal Structure of Iridescent Shark Catfish Cadherin-23 EC1-2 and Protocadherin-15 EC1-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AlphaFold2 Model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.2 M CaCl2,
0.1 M HEPES pH 7.5,
30% PEG 4000
Crystal Properties Matthews coefficient Solvent content 3.8 67.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.816 α = 90 b = 75.816 β = 90 c = 242.68 γ = 120
Symmetry Space Group P 32 2 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 X 16M 2022-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97934 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.594 44.599 100 0.975 12.907 28.1 26033
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64 99.8 0.95 6.53 20.7
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 AlphaFold2 Model 2.594 44.599 25954 1255 99.792 0.204 0.2019 0.2075 0.2424 0.2421 62.724
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] 3.185 1.593 3.185 -10.332
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.564 r_dihedral_angle_6_deg 15.534 r_dihedral_angle_3_deg 14.654 r_lrange_it 10.799 r_lrange_other 10.798 r_scangle_it 8.709 r_scangle_other 8.708 r_dihedral_angle_1_deg 7.641 r_mcangle_other 7.536 r_mcangle_it 7.535
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.564 r_dihedral_angle_6_deg 15.534 r_dihedral_angle_3_deg 14.654 r_lrange_it 10.799 r_lrange_other 10.798 r_scangle_it 8.709 r_scangle_other 8.708 r_dihedral_angle_1_deg 7.641 r_mcangle_other 7.536 r_mcangle_it 7.535 r_scbond_it 6.544 r_scbond_other 6.423 r_mcbond_it 5.481 r_mcbond_other 5.481 r_angle_refined_deg 1.526 r_angle_other_deg 0.494 r_symmetry_nbd_refined 0.417 r_nbd_other 0.272 r_metal_ion_refined 0.27 r_nbd_refined 0.199 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.157 r_xyhbond_nbd_refined 0.145 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3479 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing