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Crystal structure of strain-specific glycan-dependent CD4 binding site-directed neutralizing antibody CAP257-RH1, in complex with HIV-1 strain RHPA gp120 core with an oligomannose N276 glycan.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JZZ 4JZZ, 4HPY, 1NL0 experimental model PDB 4HPY 4JZZ, 4HPY, 1NL0 experimental model PDB 1NL0 4JZZ, 4HPY, 1NL0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298.15 0.1M HEPES (pH7.5)
8% PEG4000
10% Isopropanol
200U/mL Endo H
25% 2-Methyl-2,4-pentanediol as cryoprotectant
Crystal Properties Matthews coefficient Solvent content 2.67 53.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.176 α = 90 b = 71.139 β = 90 c = 190.596 γ = 90
Symmetry Space Group P 21 21 21
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 2014-08-23 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) 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 3.2 50 81.9 0.102 9.6 3.5 13003 90.23
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.27 33.1 0.381 0.766 2.3
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 4JZZ, 4HPY, 1NL0 3.2092 47.658 1.35 12967 646 81.99 0.2308 0.2287 0.2328 0.2689 0.2729 116.9047
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 8.248 f_angle_d 0.563 f_chiral_restr 0.041 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5801 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 533
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data collection HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction