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Crystal structure of broadly neutralizing VH1-46 germline-derived CD4-binding site-directed antibody CH235 in complex with HIV-1 clade A/E 93TH057 gp120
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RWY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 25% (w/v) of PEG2000,
0.2 M of Li2SO4, 0.1 M of Tris-HCl pH 8.5 and 5% (v/v) of isopropanol
Crystal Properties Matthews coefficient Solvent content 3.24 61.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.429 α = 90 b = 123.429 β = 90 c = 127.332 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 MARMOSAIC 300 mm CCD 2014-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.89 40.935 98.5 0.17 0.12 8.1 2.6 48360 48335
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 2.89 3 99.2 0.65 1.9 2
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 4RWY 2.8911 40.935 2 48335 2440 99.68 0.1825 0.18 0.1826 0.2319 0.235
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 11.268 f_angle_d 0.638 f_chiral_restr 0.036 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11932 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 393
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing