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Crystal Structure of Mouse Protocadherin-15 EC4-7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5T4M 5t4m, 5tpk experimental model PDB 5TPK 5t4m, 5tpk
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.1 M Tris pH 8.5
2.0 M MgAc
23% PEG 400
Crystal Properties Matthews coefficient Solvent content 4.79 74.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.863 α = 90 b = 78.863 β = 90 c = 289.469 γ = 90
Symmetry Space Group P 43 21 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 2015-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97910 APS 24-ID-C
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 3.35 76.09 98.5 0.134 16.9 11.2 14064
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 3.35 3.41 86.4 0.601 2.5 7.2
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 5t4m, 5tpk 3.35 76.09 13124 648 98.47 0.22955 0.22705 0.2291 0.27884 0.2732 RANDOM 120.669
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] 9.58 9.58 -19.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.838 r_dihedral_angle_4_deg 19.417 r_dihedral_angle_3_deg 17.981 r_dihedral_angle_1_deg 7.721 r_long_range_B_refined 7.047 r_long_range_B_other 7.047 r_scangle_other 4.507 r_mcangle_it 4.478 r_mcangle_other 4.478 r_mcbond_it 2.744
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.838 r_dihedral_angle_4_deg 19.417 r_dihedral_angle_3_deg 17.981 r_dihedral_angle_1_deg 7.721 r_long_range_B_refined 7.047 r_long_range_B_other 7.047 r_scangle_other 4.507 r_mcangle_it 4.478 r_mcangle_other 4.478 r_mcbond_it 2.744 r_mcbond_other 2.743 r_scbond_it 2.645 r_scbond_other 2.644 r_angle_refined_deg 1.62 r_angle_other_deg 1.021 r_chiral_restr 0.094 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 3118 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing