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Crystal structure of the ADCC potent antibody DH677.3 Fab elicited in the RV305 vaccine trial.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QEG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294 20% PEG 3000
100 mM HEPES pH 7.5
200 mM sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.51 51.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.658 α = 90 b = 70.52 β = 98.33 c = 84.305 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M 2018-01-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.62 50 98 0.15 0.096 0.99 13 3.4 28247
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.62 2.67 98 0.391 0.252 0.84 2.6 3.2
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 3QEG 2.62 43.03 26929 1308 97.85 0.20152 0.19859 0.1988 0.26134 0.2607 RANDOM 37.691
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] -0.71 -2.07 1.89 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.485 r_dihedral_angle_3_deg 18.387 r_dihedral_angle_4_deg 17.948 r_dihedral_angle_1_deg 7.286 r_long_range_B_refined 3.117 r_long_range_B_other 3.106 r_angle_refined_deg 1.416 r_scangle_other 1.399 r_angle_other_deg 1.289 r_mcangle_it 1.057
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.485 r_dihedral_angle_3_deg 18.387 r_dihedral_angle_4_deg 17.948 r_dihedral_angle_1_deg 7.286 r_long_range_B_refined 3.117 r_long_range_B_other 3.106 r_angle_refined_deg 1.416 r_scangle_other 1.399 r_angle_other_deg 1.289 r_mcangle_it 1.057 r_mcangle_other 1.057 r_scbond_it 0.809 r_scbond_other 0.809 r_mcbond_it 0.608 r_mcbond_other 0.608 r_chiral_restr 0.057 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6563 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing