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IgE-Fc in complex with DARPins E2_79 and E3_53
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GT7 4gt7, 4grg, 4ycw experimental model PDB 4GRG 4gt7, 4grg, 4ycw experimental model PDB 4YCW 4gt7, 4grg, 4ycw
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 291 E3_53, E2_79, and IgE-Fc3-4 were mixed in equimolar ratios with E3_53 and E2_79, and intact complexes were purified by SEC in 20 mM Tris-HCl, pH 8.0, 50mM NaCl and concentrated to 7mg/ml and mixed 1:1 with acetate buffer pH 4.6, 43% ethylene glycol w/v in hanging drops
Crystal Properties Matthews coefficient Solvent content 2.78 55.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.908 α = 90 b = 137.793 β = 105.68 c = 88.25 γ = 90
Symmetry Space Group P 1 21 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 6M 2016-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
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 2.8 38.74 98.65 0.1948 0.983 5.07 3.7 29053
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 98.37 0.8242 0.577 0.66
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4gt7, 4grg, 4ycw 2.8 38.74 1.33 29050 1278 98.7 0.2152 0.2134 0.2161 0.2563 0.2598 61.1866
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.162 f_angle_d 0.998 f_chiral_restr 0.067 f_plane_restr 0.008 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7371 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 116
Software Software Software Name Purpose PHENIX refinement XDS data scaling PDB_EXTRACT data extraction XDS data reduction PHENIX phasing