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Crystal structure of human IZUMO1-JUNO complex (crystal form 2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JK9 5JK9, 5JKA experimental model PDB 5JKA 5JK9, 5JKA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.0 M (NH4)2SO4, 1.0 M KCl, 0.1 M HEPES-NaOH pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.32 62.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.604 α = 90 b = 65.377 β = 104.24 c = 77.199 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 2M-F 2016-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0000 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.9 50 99.9 21.6 6.6 15805
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 5JK9, 5JKA 2.9 50 15006 799 99.77 0.22169 0.22008 0.2216 0.2508 0.247 RANDOM 88.915
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] -5.4 -1.37 4.18 1.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.455 r_dihedral_angle_3_deg 17.272 r_dihedral_angle_4_deg 15.595 r_long_range_B_refined 14.84 r_long_range_B_other 14.839 r_scangle_other 9.269 r_mcangle_it 7.874 r_mcangle_other 7.872 r_dihedral_angle_1_deg 6.777 r_scbond_it 5.919
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.455 r_dihedral_angle_3_deg 17.272 r_dihedral_angle_4_deg 15.595 r_long_range_B_refined 14.84 r_long_range_B_other 14.839 r_scangle_other 9.269 r_mcangle_it 7.874 r_mcangle_other 7.872 r_dihedral_angle_1_deg 6.777 r_scbond_it 5.919 r_scbond_other 5.918 r_mcbond_other 5.062 r_mcbond_it 5.061 r_angle_refined_deg 1.564 r_angle_other_deg 0.983 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 3480 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing