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Crystal structure of human IgG-Fc in complex with aglycan and optimized 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, HANGING DROP 7.4 293.15 20mM Tris-HCl, 100mM NaCl, 14% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.19 61.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.79 α = 90 b = 101.42 β = 90 c = 122.6 γ = 90
Symmetry Space Group P 21 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 CCD ADSC QUANTUM 315r 2016-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.71 46.9 100 0.121 0.058 0.995 9.6 5.9 25395
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.71 2.84 100 0.848 0.37 0.842 2 6.2
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 2.71 46.9 24076 1260 99.93 0.21197 0.2087 0.2145 0.27294 0.275 RANDOM 54.098
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] 5.58 -3.76 -1.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.606 r_dihedral_angle_3_deg 18.154 r_dihedral_angle_4_deg 18.009 r_dihedral_angle_1_deg 7.584 r_long_range_B_refined 4.043 r_long_range_B_other 4.039 r_scangle_other 2.709 r_mcangle_it 2.48 r_mcangle_other 2.479 r_angle_refined_deg 1.984
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.606 r_dihedral_angle_3_deg 18.154 r_dihedral_angle_4_deg 18.009 r_dihedral_angle_1_deg 7.584 r_long_range_B_refined 4.043 r_long_range_B_other 4.039 r_scangle_other 2.709 r_mcangle_it 2.48 r_mcangle_other 2.479 r_angle_refined_deg 1.984 r_scbond_it 1.638 r_scbond_other 1.637 r_mcbond_it 1.519 r_mcbond_other 1.519 r_angle_other_deg 1.063 r_chiral_restr 0.099 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 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 4750 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 210
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing