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Crystal structure of the non-neutralizing and ADCC-potent C11-like antibody N12-i3 in complex with HIV-1 clade A/E gp120, the CD4 mimetic M48U1, and the antibody N5-i5.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H8W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 294 15% PEG 2000 MME
0.1 M Tris-HCl pH 8.0
0.1 M KCl
Crystal Properties Matthews coefficient Solvent content 2.57 52.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 311.018 α = 90 b = 53.291 β = 128.89 c = 223.577 γ = 90
Symmetry Space Group C 1 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 PILATUS 2M Rh coated flat bent mirror 2015-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.97947 SSRL BL7-1
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 2.92 50 99.8 0.184 6 3.7 62153
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 2.92 3 99.9 0.923 1.1 3.8
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 4H8W 2.92 50 59072 3079 98.51 0.23426 0.23132 0.2315 0.29191 0.2913 RANDOM 72.496
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] 0.25 0.88 -1.9 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.497 r_dihedral_angle_4_deg 17.856 r_dihedral_angle_3_deg 16.51 r_dihedral_angle_1_deg 7.095 r_long_range_B_refined 3.86 r_long_range_B_other 3.86 r_angle_refined_deg 1.393 r_scangle_other 1.345 r_angle_other_deg 0.97 r_mcangle_it 0.875
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.497 r_dihedral_angle_4_deg 17.856 r_dihedral_angle_3_deg 16.51 r_dihedral_angle_1_deg 7.095 r_long_range_B_refined 3.86 r_long_range_B_other 3.86 r_angle_refined_deg 1.393 r_scangle_other 1.345 r_angle_other_deg 0.97 r_mcangle_it 0.875 r_mcangle_other 0.875 r_scbond_it 0.732 r_scbond_other 0.732 r_mcbond_it 0.493 r_mcbond_other 0.493 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 18756 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 296
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing