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Crystal Structure of Human Protocadherin-15 EC2-3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4APX 4APX, 5T4M experimental model PDB 5T4M 4APX, 5T4M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277.15 0.1 M HEPES (pH 7.5), 0.1 M KCl, 15% PEG 6000
Crystal Properties Matthews coefficient Solvent content 3.13 60.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.761 α = 90 b = 147.625 β = 101.16 c = 77.034 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 PILATUS 6M-F 2015-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97920 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 2.64 50 96.4 0.098 10.625 2.6 42598 45.7
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 2.64 2.69 95 0.581 1.7 2.4
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 4APX, 5T4M 2.64 50 39053 1962 96.1 0.21671 0.21523 0.2167 0.2464 0.2471 RANDOM 54.895
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] -3.22 1.4 -4.04 6.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.882 r_dihedral_angle_4_deg 18.675 r_dihedral_angle_3_deg 15.8 r_dihedral_angle_1_deg 7.149 r_long_range_B_refined 3.857 r_long_range_B_other 3.834 r_scangle_other 2.36 r_mcangle_it 2.133 r_mcangle_other 2.133 r_angle_refined_deg 1.689
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.882 r_dihedral_angle_4_deg 18.675 r_dihedral_angle_3_deg 15.8 r_dihedral_angle_1_deg 7.149 r_long_range_B_refined 3.857 r_long_range_B_other 3.834 r_scangle_other 2.36 r_mcangle_it 2.133 r_mcangle_other 2.133 r_angle_refined_deg 1.689 r_scbond_it 1.419 r_scbond_other 1.419 r_mcbond_it 1.308 r_mcbond_other 1.308 r_angle_other_deg 1.028 r_chiral_restr 0.098 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 7135 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing