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Crystal structure of a human afucosylated IgG1 Fc expressed in tobacco plants (Nicotiana benthamiana)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AVE PDB entry 3AVE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 294 15% PEG4000, 0.1 M HEPES, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.86 56.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.7 α = 90 b = 80.32 β = 90 c = 136.99 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 PIXEL DECTRIS EIGER X 9M 2019-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.9795 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.6 50 88 0.083 0.047 0.99 8.3 3.6 15294
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.74 90.2 0.902 0.497 0.68 1.8 3.6
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 FREE R-VALUE PDB entry 3AVE 2.6 50 1.34 15258 768 87.07 0.224 0.2212 0.2265 0.2755 0.275
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 7.174 f_angle_d 1.581 f_chiral_restr 0.071 f_bond_d 0.014 f_plane_restr 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3324 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 200
Software Software Software Name Purpose PHENIX refinement REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing