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Crystal Structure of Mouse Protocadherin-15 EC7-8 V875A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XHZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 0.2M AMMONIUM CHLORIDE, 10% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.26 45.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.796 α = 90 b = 22.99 β = 97.27 c = 70.741 γ = 90
Symmetry Space Group C 1 2 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 2015-03-22 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 70.17 96.5 0.045 23.12 3.1 15280 33
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 2.03 82.1 0.141 5.4 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4XHZ 2 70.17 14026 711 96.36 0.19177 0.18995 0.22897 0.2383 RANDOM 40.26
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] -1.95 -1.37 0.09 2.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.743 r_dihedral_angle_4_deg 20.062 r_dihedral_angle_3_deg 12.302 r_dihedral_angle_1_deg 6.359 r_long_range_B_refined 5.006 r_long_range_B_other 4.903 r_mcangle_it 1.603 r_mcangle_other 1.602 r_scangle_other 1.433 r_angle_refined_deg 1.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.743 r_dihedral_angle_4_deg 20.062 r_dihedral_angle_3_deg 12.302 r_dihedral_angle_1_deg 6.359 r_long_range_B_refined 5.006 r_long_range_B_other 4.903 r_mcangle_it 1.603 r_mcangle_other 1.602 r_scangle_other 1.433 r_angle_refined_deg 1.315 r_mcbond_other 0.917 r_mcbond_it 0.916 r_angle_other_deg 0.88 r_scbond_it 0.848 r_scbond_other 0.848 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 1572 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing