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Crystal Structure of Mouse Protocadherin-15 EC9-10
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 7.5 277.15 0.095M HEPES (pH7.5), 0.19M CaCl2, 26.6% v/v PEG 400
Crystal Properties Matthews coefficient Solvent content 5.71 78.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.541 α = 90 b = 143.541 β = 90 c = 95.599 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2015-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 50 100 0.256 0.91 6.96 5.9 31590 69.9
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 3.41 100 0.931 2.03 5.8
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 4XHZ 3.35 46.98 30204 1367 99.94 0.15943 0.15789 0.1267 0.1959 0.1479 RANDOM 77.308
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] 6.01 6.01 -12.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.926 r_dihedral_angle_4_deg 17.113 r_dihedral_angle_3_deg 15.094 r_long_range_B_refined 6.015 r_long_range_B_other 6.015 r_dihedral_angle_1_deg 5.461 r_mcangle_it 2.682 r_mcangle_other 2.682 r_scangle_other 2.309 r_mcbond_it 1.597
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.926 r_dihedral_angle_4_deg 17.113 r_dihedral_angle_3_deg 15.094 r_long_range_B_refined 6.015 r_long_range_B_other 6.015 r_dihedral_angle_1_deg 5.461 r_mcangle_it 2.682 r_mcangle_other 2.682 r_scangle_other 2.309 r_mcbond_it 1.597 r_mcbond_other 1.597 r_scbond_it 1.348 r_scbond_other 1.348 r_angle_refined_deg 1.078 r_angle_other_deg 0.688 r_chiral_restr 0.06 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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 6986 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing