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Crystal Structure of Broadly Neutralizing Antibody CH03, Isolated from Donor CH0219, in Complex with Scaffolded Trimeric HIV-1 Env V1V2 Domain from the Clade C Superinfecting Strain of Donor CAP256.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TCL 3TCL, 4TVP and 1VH8 experimental model PDB 4TVP 3TCL, 4TVP and 1VH8 experimental model PDB 1VH8 3TCL, 4TVP and 1VH8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 10% PEG8000, .1M CaCl, 20% MPD, .1M Na Acetate pH 5.5, frozen in 15% sucrose as cryoprotectant
Crystal Properties Matthews coefficient Solvent content 2.74 55.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.693 α = 90 b = 98.211 β = 112.82 c = 170.629 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 CCD MARMOSAIC 300 mm CCD 2014-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 99.7 7.3 3.4 44647
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3TCL, 4TVP and 1VH8 3.105 41.987 1.33 44635 2004 99.15 0.2109 0.2085 0.2089 0.2591 0.2605
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.706 f_angle_d 0.869 f_chiral_restr 0.073 f_bond_d 0.005 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14297 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 743
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing