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Crystal structure of human IZUMO1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 12-15% (w/v) PEG6000, 0.1 M sodium citrate pH 5.6
Crystal Properties Matthews coefficient Solvent content 2.87 57.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.936 α = 77.65 b = 75.067 β = 79.11 c = 108.885 γ = 70.66
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 2015-12-20 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 2.1 50 97.6 21.6 3.5 106951
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MIR THROUGHOUT 2.1 50 101240 5249 97.43 0.19615 0.19431 0.23057 0.2324 RANDOM 48.7
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] -0.34 1.63 -1.38 0.32 0.7 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.857 r_dihedral_angle_3_deg 15.861 r_dihedral_angle_4_deg 14.534 r_long_range_B_other 10.839 r_long_range_B_refined 10.835 r_scangle_other 9.009 r_scbond_it 6.183 r_scbond_other 6.182 r_dihedral_angle_1_deg 6.054 r_mcangle_it 5.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.857 r_dihedral_angle_3_deg 15.861 r_dihedral_angle_4_deg 14.534 r_long_range_B_other 10.839 r_long_range_B_refined 10.835 r_scangle_other 9.009 r_scbond_it 6.183 r_scbond_other 6.182 r_dihedral_angle_1_deg 6.054 r_mcangle_it 5.95 r_mcangle_other 5.949 r_mcbond_it 4.43 r_mcbond_other 4.429 r_angle_refined_deg 1.615 r_angle_other_deg 0.97 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 11088 Nucleic Acid Atoms Solvent Atoms 537 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling autoSHARP phasing