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Crystal structure of the stabilized inner domain of clade A/E HIV-1 gp120 from E. coli in complex with the 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 PEG8000
0.1 M Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.18 43.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.801 α = 90 b = 211.8 β = 90 c = 72.898 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 PIXEL PSI PILATUS 6M 2015-01-23 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) 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 50 87.1 0.163 9.5 5.8 23714 20655
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 3.05 86.7 0.88 1.2 5.8
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 3TNM and 4RQH 3.02 50 19540 1087 86.18 0.23034 0.22724 0.2285 0.28774 0.2838 RANDOM 88.657
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] -1.53 0.19 1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.787 r_dihedral_angle_3_deg 15.925 r_dihedral_angle_4_deg 14.994 r_dihedral_angle_1_deg 8.29 r_long_range_B_refined 4.984 r_long_range_B_other 4.984 r_mcangle_it 1.72 r_mcangle_other 1.72 r_angle_refined_deg 1.448 r_scangle_other 1.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.787 r_dihedral_angle_3_deg 15.925 r_dihedral_angle_4_deg 14.994 r_dihedral_angle_1_deg 8.29 r_long_range_B_refined 4.984 r_long_range_B_other 4.984 r_mcangle_it 1.72 r_mcangle_other 1.72 r_angle_refined_deg 1.448 r_scangle_other 1.017 r_angle_other_deg 1.015 r_mcbond_other 0.918 r_mcbond_it 0.917 r_scbond_it 0.497 r_scbond_other 0.497 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.003 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 8600 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX refinement CNS refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing