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Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4APX 4APX, 5ULY experimental model PDB 5ULY 4APX, 5ULY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.7 277 0.1 M HEPES pH 7.7, 66% MPD, 4% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.97 58.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.894 α = 90 b = 116.516 β = 90 c = 99.889 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 PILATUS 6M-F 2017-11-07 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) 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 3.15 50 99.4 0.362 0.119 6.8 9 9312
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.15 3.2 99.8 1.384 0.616 5.2
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 4APX, 5ULY 3.15 49.99 8791 442 97.64 0.21806 0.21454 0.2185 0.28841 0.2944 RANDOM 74.744
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] -0.27 -3.95 4.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.187 r_dihedral_angle_4_deg 21.728 r_dihedral_angle_3_deg 17.252 r_dihedral_angle_1_deg 8.673 r_long_range_B_refined 7 r_long_range_B_other 7 r_scangle_other 4.727 r_mcangle_it 4.52 r_mcangle_other 4.52 r_scbond_it 2.848
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.187 r_dihedral_angle_4_deg 21.728 r_dihedral_angle_3_deg 17.252 r_dihedral_angle_1_deg 8.673 r_long_range_B_refined 7 r_long_range_B_other 7 r_scangle_other 4.727 r_mcangle_it 4.52 r_mcangle_other 4.52 r_scbond_it 2.848 r_scbond_other 2.847 r_mcbond_it 2.781 r_mcbond_other 2.78 r_angle_refined_deg 1.361 r_angle_other_deg 0.817 r_chiral_restr 0.058 r_bond_refined_d 0.009 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 2629 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing