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Crystal Structure of Mouse Protocadherin-15 EC6-7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TPK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 30% PEG1500
Crystal Properties Matthews coefficient Solvent content 8.06 84.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.981 α = 90 b = 110.981 β = 90 c = 206.024 γ = 120
Symmetry Space Group P 62 2 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 EIGER X 16M 2017-06-15 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) 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 2.94 96.11 98.1 0.131 10.9 7.7 16643
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.95 3 96.9 2 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 5tpk 2.94 96.11 15473 841 98.28 0.21797 0.21668 0.2241 0.24171 0.247 RANDOM 104.239
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] 3.88 1.94 3.88 -12.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.468 r_dihedral_angle_4_deg 16.418 r_dihedral_angle_3_deg 15.23 r_long_range_B_other 9.081 r_long_range_B_refined 9.056 r_scangle_other 6.638 r_dihedral_angle_1_deg 6.631 r_mcangle_other 6.609 r_mcangle_it 6.584 r_mcbond_it 4.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.468 r_dihedral_angle_4_deg 16.418 r_dihedral_angle_3_deg 15.23 r_long_range_B_other 9.081 r_long_range_B_refined 9.056 r_scangle_other 6.638 r_dihedral_angle_1_deg 6.631 r_mcangle_other 6.609 r_mcangle_it 6.584 r_mcbond_it 4.097 r_scbond_it 3.993 r_scbond_other 3.987 r_mcbond_other 3.903 r_angle_refined_deg 1.321 r_angle_other_deg 0.921 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 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 1594 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing