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Crystal structure of mouse Protocadherin-15 EC9-MAD12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6BXZ 6BXZ, 4XHZ experimental model PDB 4XHZ 6BXZ, 4XHZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.1 M HEPES sodium salt, 30% (w/v) MPD, 5% (w/v) PEG4000
Crystal Properties Matthews coefficient Solvent content 4.77 74.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.507 α = 90 b = 170.059 β = 90 c = 91.528 γ = 90
Symmetry Space Group C 2 2 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 EIGER X 16M 2018-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9792 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.2 100 99.5 0.166 14.529 9.8 16630
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.26 94.8 0.808 2.222 4.7
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 (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 6BXZ, 4XHZ 3.23 45.81 15743 790 99.18 0.17854 0.17568 0.182 0.2339 0.2424 RANDOM 94.283
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] 3.33 1.9 -5.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.253 r_dihedral_angle_4_deg 19.287 r_dihedral_angle_3_deg 18.554 r_long_range_B_other 12.486 r_long_range_B_refined 12.48 r_scangle_other 10.234 r_mcangle_it 8.767 r_mcangle_other 8.766 r_dihedral_angle_1_deg 8.228 r_scbond_it 6.659
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.253 r_dihedral_angle_4_deg 19.287 r_dihedral_angle_3_deg 18.554 r_long_range_B_other 12.486 r_long_range_B_refined 12.48 r_scangle_other 10.234 r_mcangle_it 8.767 r_mcangle_other 8.766 r_dihedral_angle_1_deg 8.228 r_scbond_it 6.659 r_scbond_other 6.65 r_mcbond_it 5.993 r_mcbond_other 5.974 r_angle_refined_deg 1.397 r_angle_other_deg 0.809 r_chiral_restr 0.06 r_bond_refined_d 0.008 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 3476 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing