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Crystal structure of the ADCC-potent antibody N60-i3 Fab in complex with HIV-1 Clade A/E gp120 W69A/S115W mutant and M48U1.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RFO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 294 10-16% PEG 8000,
0.1 M TRIS-HCL PH 8.5,
65 MM NACL
Crystal Properties Matthews coefficient Solvent content 2.93 58.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.191 α = 90 b = 101.944 β = 90 c = 108.747 γ = 90
Symmetry Space Group P 21 21 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 CCD MARMOSAIC 325 mm CCD RH Coated Flat mirror 2016-01-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 0.97946 SSRL BL14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.98 50 87.6 0.22 5.1 4 19540
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.98 3.05 67.6 0.676 1.2 3.7
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 4RFO 2.98 50 18481 1007 87.6 0.2518 0.2488 0.2483 0.30602 0.3025 RANDOM 51.54
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] -2.03 -0.63 2.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.653 r_dihedral_angle_3_deg 22.349 r_dihedral_angle_4_deg 21.018 r_dihedral_angle_1_deg 8.232 r_long_range_B_refined 6.503 r_long_range_B_other 6.502 r_scangle_other 2.257 r_mcangle_it 2.211 r_mcangle_other 2.211 r_angle_refined_deg 1.981
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.653 r_dihedral_angle_3_deg 22.349 r_dihedral_angle_4_deg 21.018 r_dihedral_angle_1_deg 8.232 r_long_range_B_refined 6.503 r_long_range_B_other 6.502 r_scangle_other 2.257 r_mcangle_it 2.211 r_mcangle_other 2.211 r_angle_refined_deg 1.981 r_scbond_it 1.344 r_scbond_other 1.344 r_mcbond_it 1.249 r_mcbond_other 1.249 r_angle_other_deg 1.219 r_chiral_restr 0.099 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.003 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 6036 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 148
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing