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Crystal structure of a V2p-reactive RV144 vaccine-like antibody, CAP228-16H, in complex with a scaffolded autologous V1V2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FY0 D_1200009079
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298.15 0.1 M Tris HCl (pH8.5), 5% PEG4000, 2 M sodium chloride, 10% butanol, and cryoprotected in 25% 2,3-Butanediol
Crystal Properties Matthews coefficient Solvent content 2.37 48.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.991 α = 90 b = 73.987 β = 91.98 c = 191.034 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 2016-10-15 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) Rpim I (All) CC (Half) 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 3.21 50 89.7 0.156 0.098 0.936 6.8 3.2 19842
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.21 3.27 89.4 0.791 0.5 0.812 2 3.2
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 D_1200009079 3.132 40.971 1.34 17782 1804 87.28 0.2259 0.2207 0.2243 0.2707 0.268
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 11.172 f_angle_d 0.681 f_chiral_restr 0.047 f_plane_restr 0.005 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7653 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing Coot model building