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Crystal structure of human Fab CAP256-VRC26.25, a potent V1V2-directed HIV-1 broadly neutralizing antibody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OD1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 Crystals grown in a reservoir solution of 23% PEG 8000 and 0.1M HEPES pH 7.5 and flash frozen in liquid nitrogen with 20% PEG 400 as a cryoprotectant
Crystal Properties Matthews coefficient Solvent content 2.54 51.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.016 α = 90 b = 77.027 β = 90 c = 85.227 γ = 90
Symmetry Space Group P 21 2 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 2014-11-26 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) 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 1.954 42.614 90.8 0.114 0.125 0.049 10.2 5.3 33667 24.79
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2.04 50.4 0.329 0.436 0.283 0.817 1.6 1841
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 4OD1 1.954 42.614 1.35 33622 1684 89.78 0.1716 0.1693 0.1711 0.2146 0.2157 33.7624
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 11.607 f_angle_d 0.889 f_chiral_restr 0.055 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3484 Nucleic Acid Atoms Solvent Atoms 333 Heterogen Atoms 72
Software Software Software Name Purpose HKL-2000 data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHENIX phasing