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Crystal structure of the stabilized inner domain of clade A/E HIV-1 gp120 in complex with the ADCC mediating ANTI-HIV-1 antibody A32
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TNM 3TNM and 4RQH experimental model PDB 4RQH 3TNM and 4RQH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 18-22% PEG 6000 or 8000
0.1 M Tris-HCl pH 8.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.742 α = 90 b = 208.209 β = 90 c = 73.22 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 ADSC QUANTUM 315 2014-11-28 M SINGLE WAVELENGTH 2 2 x-ray 100 PIXEL PSI PILATUS 6M 2015-01-23 M SINGLE WAVELENGTH 3 3 100
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.12789 SSRL BL7-1 2 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) 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 3.1 50 93.2 0.186 14.6 8.3 21415 19959
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 3.1 3.15 96.8 0.955 1.3 8.3
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 3TNM and 4RQH 3.1 50 18913 1021 91.54 0.2346 0.23178 0.2305 0.28937 0.2851 RANDOM 94.206
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] -0.92 -0.36 1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.47 r_dihedral_angle_3_deg 17.248 r_dihedral_angle_4_deg 13.927 r_dihedral_angle_1_deg 8.57 r_long_range_B_refined 4.03 r_long_range_B_other 4.03 r_angle_refined_deg 1.527 r_mcangle_it 1.486 r_mcangle_other 1.486 r_scangle_other 1.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.47 r_dihedral_angle_3_deg 17.248 r_dihedral_angle_4_deg 13.927 r_dihedral_angle_1_deg 8.57 r_long_range_B_refined 4.03 r_long_range_B_other 4.03 r_angle_refined_deg 1.527 r_mcangle_it 1.486 r_mcangle_other 1.486 r_scangle_other 1.103 r_angle_other_deg 1.016 r_mcbond_it 0.814 r_mcbond_other 0.814 r_scbond_it 0.59 r_scbond_other 0.59 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 8470 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX refinement CNS refinement PHASER phasing HKL-2000 data scaling