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Genetic and structural basis of 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, HANGING DROP 8 293 Equal volumes of a protein (in 25 mM Tris (pH 8.0), 100 mM NaCl) and well solution (1.5 M NaH2PO4.H2O.K2HPO4, pH 8.0) were combined.
Crystal Properties Matthews coefficient Solvent content 2.36 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.492 α = 90 b = 101.492 β = 90 c = 78.159 γ = 120
Symmetry Space Group P 32 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 2017-04-11 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 1.55 38.31 100 0.091 0.093 0.021 0.999 17.2 18.9 67630
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 1.55 1.58 99.9 1.757 1.822 0.475 0.465 14.3
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 generic Fab 1.55 38.31 64307 3288 99.96 0.1298 0.1276 0.1278 0.1747 0.1752 RANDOM 27.962
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] 0.17 0.08 0.17 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.129 r_dihedral_angle_4_deg 20.351 r_dihedral_angle_3_deg 12.178 r_dihedral_angle_1_deg 7.237 r_rigid_bond_restr 3.296 r_angle_refined_deg 1.681 r_angle_other_deg 1.452 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.129 r_dihedral_angle_4_deg 20.351 r_dihedral_angle_3_deg 12.178 r_dihedral_angle_1_deg 7.237 r_rigid_bond_restr 3.296 r_angle_refined_deg 1.681 r_angle_other_deg 1.452 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3196 Nucleic Acid Atoms Solvent Atoms 347 Heterogen Atoms 45
Software Software Software Name Purpose MOSFLM data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction