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Crystal structure of antibody Fab G001-0087 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 Modeller 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 3000, 0.1 M sodium citrate pH 5.5, with addition of 10% (v/v) ethylene glycol
Crystal Properties Matthews coefficient Solvent content 4.01 69.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.5 α = 90 b = 136.171 β = 90 c = 152.944 γ = 90
Symmetry Space Group I 2 2 2
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 2022-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
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 2.58 50 99.3 0.98 12.3 10.5 33387 44.32
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 2.58 2.64 0.429
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 2.58 47.74 1.33 33110 1631 97.5 0.239 0.2383 0.2373 0.2526 0.2511 48.13
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 11.8268 f_angle_d 0.5503 f_chiral_restr 0.0452 f_plane_restr 0.0049 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4516 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 28
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing