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Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6MFO 6MFO, 4AQ8 experimental model PDB 4AQ8 6MFO, 4AQ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.1 M Imidazole pH 6.8,
46% MPD
Crystal Properties Matthews coefficient Solvent content 3.52 65.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.792 α = 90 b = 65.397 β = 99.12 c = 190.015 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 EIGER X 16M 2018-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.9 50 93.2 0.115 0.055 12.33 5.2 41847
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.95 86.5 0.236 4.4
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 6MFO, 4AQ8 2.9 49.52 37058 1909 92.36 0.22605 0.22464 0.2264 0.25332 0.2566 RANDOM 75.813
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] -7.42 -49.81 63.34 -55.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.553 r_dihedral_angle_4_deg 17.897 r_dihedral_angle_3_deg 15.887 r_dihedral_angle_1_deg 8.358 r_long_range_B_refined 2.783 r_long_range_B_other 2.742 r_angle_refined_deg 1.639 r_angle_other_deg 1.28 r_mcangle_it 0.433 r_mcangle_other 0.433
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.553 r_dihedral_angle_4_deg 17.897 r_dihedral_angle_3_deg 15.887 r_dihedral_angle_1_deg 8.358 r_long_range_B_refined 2.783 r_long_range_B_other 2.742 r_angle_refined_deg 1.639 r_angle_other_deg 1.28 r_mcangle_it 0.433 r_mcangle_other 0.433 r_scangle_other 0.417 r_scbond_it 0.246 r_scbond_other 0.246 r_mcbond_it 0.235 r_mcbond_other 0.235 r_chiral_restr 0.075 r_gen_planes_refined 0.013 r_bond_refined_d 0.012 r_gen_planes_other 0.002 r_bond_other_d 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 8699 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing