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Crystal structure of a human fucosylated 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 2.89 57.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.86 α = 90 b = 79.92 β = 90 c = 138.54 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 2019-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.920 NSLS-II 17-ID-1
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 2.1 50 98.7 0.097 0.061 0.99 5.4 3.3 32561
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 2.1 2.21 99.3 0.775 0.479 0.5 1 3.4
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 2.1 46.91 0.08 58447 2893 93.65 0.2096 0.2075 0.2077 0.2499 0.2536
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 8.392 f_angle_d 1.102 f_chiral_restr 0.06 f_bond_d 0.01 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3340 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 236
Software Software Software Name Purpose PHENIX refinement REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing