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Crystal structure of human IZUMO1-JUNO complex (crystal form 3)
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 20% PEG4000, 0.2 M Li2SO4, 0.1 M MES-NaOH pH 6.0
Crystal Properties Matthews coefficient Solvent content 3.07 59.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.182 α = 90 b = 141.776 β = 90 c = 144.861 γ = 90
Symmetry Space Group P 2 21 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 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 2.86 48.3 100 28.5 13.2 31399
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 2.86 48.3 29880 1468 99.96 0.20429 0.20265 0.206 0.23817 0.2438 RANDOM 86.849
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] 1.84 -1.49 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.872 r_dihedral_angle_4_deg 21.38 r_dihedral_angle_3_deg 17.46 r_long_range_B_refined 13.534 r_long_range_B_other 13.534 r_scangle_other 9.767 r_mcangle_other 8.501 r_mcangle_it 8.499 r_dihedral_angle_1_deg 6.593 r_scbond_it 6.483
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.872 r_dihedral_angle_4_deg 21.38 r_dihedral_angle_3_deg 17.46 r_long_range_B_refined 13.534 r_long_range_B_other 13.534 r_scangle_other 9.767 r_mcangle_other 8.501 r_mcangle_it 8.499 r_dihedral_angle_1_deg 6.593 r_scbond_it 6.483 r_scbond_other 6.483 r_mcbond_it 5.682 r_mcbond_other 5.676 r_angle_refined_deg 1.592 r_angle_other_deg 1.132 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.004 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 6994 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing