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Crystal structure of antibody Fab G001-58 from IAVI G001 human trial in complex with a germline-targeting gp120 engineered outer domain eOD-GT8-mingly
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model SwissModel initial Fab models generated by Sisimm Repertoire Builder experimental model PDB 5IDL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 20% (w/v) PEG 3350 and 0.2 M magnesium chloride at pH 5.8
Crystal Properties Matthews coefficient Solvent content 3.37 63.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.08 α = 90 b = 174.91 β = 90 c = 93.581 γ = 90
Symmetry Space Group C 2 2 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 16M 2022-01-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-1 0.9795 SSRL BL12-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.8 50 99.1 0.987 8.3 12.8 22255 64.39
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.87 0.411
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.8 47.44 1.34 22153 1070 97.93 0.215 0.2132 0.2136 0.2494 0.25 62.73
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 13.1611 f_angle_d 0.4994 f_chiral_restr 0.0441 f_plane_restr 0.0041 f_bond_d 0.0026
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4513 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 28
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing