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Crystal structure of fucosylated IgG Fc Y296W mutant complexed with bis-glycosylated soluble form of Fc gamma receptor IIIa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AY4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 12% PEG 20000, 0.1 M MES (pH 6.5), 4% Zwittergent 3-14
Crystal Properties Matthews coefficient Solvent content 3.68 66.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.3 α = 90 b = 77.3 β = 90 c = 349.8 γ = 90
Symmetry Space Group P 41 21 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 CCD ADSC QUANTUM 315 2013-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.00000 Photon Factory BL-5A
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 2.5 46.55 99.7 0.077 23.7 13.5 37895
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.65 98.9 0.902 2.6 11.8
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 3AY4 2.5 20 35921 1890 99.54 0.22277 0.2203 0.2228 0.26991 0.2719 RANDOM 66.322
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] 0.5 0.5 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.976 r_dihedral_angle_3_deg 16.086 r_dihedral_angle_4_deg 14.742 r_long_range_B_other 9.295 r_long_range_B_refined 9.294 r_scangle_other 6.878 r_dihedral_angle_1_deg 6.761 r_mcangle_it 6.201 r_mcangle_other 6.2 r_scbond_it 4.345
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.976 r_dihedral_angle_3_deg 16.086 r_dihedral_angle_4_deg 14.742 r_long_range_B_other 9.295 r_long_range_B_refined 9.294 r_scangle_other 6.878 r_dihedral_angle_1_deg 6.761 r_mcangle_it 6.201 r_mcangle_other 6.2 r_scbond_it 4.345 r_scbond_other 4.344 r_mcbond_it 4.098 r_mcbond_other 4.098 r_angle_refined_deg 1.609 r_angle_other_deg 0.948 r_chiral_restr 0.178 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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 4653 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 299
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing