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Genomic and structural basis for the human anti-alpha-galactosyl antibody response
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N8Z Fab arm first split into variable and constant pairings
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 293 Equal volumes of protein (in 25 mM Tris, 100 mM NaCl) were combined with well solution (1 M LiCl2, 100 mM citrate (pH 4.0), 20% (w/v) PEG6000
Crystal Properties Matthews coefficient Solvent content 2.24 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.937 α = 90 b = 65.931 β = 90.91 c = 151.513 γ = 90
Symmetry Space Group C 1 2 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 EIGER X 16M 2018-08-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.31 43.46 98.6 0.112 0.123 0.05 0.995 10 5.8 37114 33.28
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.31 2.4 92.9 0.519 0.574 0.239 0.857 5.4
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 THROUGHOUT generic Fab 2.314 42.974 1.33 37093 1810 98.43 0.191 0.1889 0.1903 0.2311 0.2316 37.0057
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 3.165 f_angle_d 0.804 f_chiral_restr 0.051 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6581 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 61
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction