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Crystal Structure of Tier 2 Neutralizing Antibody DH427 from a Rhesus Macaque in Complex with HIV-1 gp120 Core
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LST HIV strain ZM176.66 gp120 core from PDB Entry 4LST, and separated Fv and Fc regions of DH427 Fab from PDB Entry 5F6H experimental model PDB 5F6H HIV strain ZM176.66 gp120 core from PDB Entry 4LST, and separated Fv and Fc regions of DH427 Fab from PDB Entry 5F6H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 1.5M ammonium sulfate and 100 mM Tris, pH 8.0
Crystal Properties Matthews coefficient Solvent content 5.1 75.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.902 α = 90 b = 162.902 β = 90 c = 229.854 γ = 120
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 2015-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97916 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 6.63 141.08 93.2 0.273 0.312 0.146 7.5 6.7 6058
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 6.63 6.8 94.1 1.1 6.6
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 HIV strain ZM176.66 gp120 core from PDB Entry 4LST, and separated Fv and Fc regions of DH427 Fab from PDB Entry 5F6H 6.63 141.08 5756 302 93.24 0.2585 0.256 0.2568 0.3046 0.3042 RANDOM 276.625
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] -1.41 -0.71 -1.41 4.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.348 r_dihedral_angle_3_deg 18.676 r_mcangle_it 17.615 r_dihedral_angle_4_deg 16.746 r_mcbond_it 9.979 r_scbond_it 9.757 r_dihedral_angle_1_deg 6.457 r_angle_refined_deg 1.389 r_chiral_restr 0.084 r_bond_refined_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.348 r_dihedral_angle_3_deg 18.676 r_mcangle_it 17.615 r_dihedral_angle_4_deg 16.746 r_mcbond_it 9.979 r_scbond_it 9.757 r_dihedral_angle_1_deg 6.457 r_angle_refined_deg 1.389 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11572 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction PHASER phasing HKL-2000 data reduction HKL-2000 data scaling Coot model building