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Crystal structure of VRC01c-HuGL2 Fab from an HIV-1 naive donor in complex with with a germline-targeting gp120 engineered outer domain eOD-GT8 at 2.16 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JPK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293.15 0.1 M citric acid (pH 4.0), 20% (w/v) PEG6000 with an overall pH 5.0 of the solution, cryo-protected with 25% glycerol
Crystal Properties Matthews coefficient Solvent content 4.06 69.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.553 α = 90 b = 138.604 β = 90 c = 147.896 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 PIXEL DECTRIS PILATUS 6M 2015-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.1542 46.45 92.5 0.067 0.902 16.2 3.9 52709 48.7
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 2.16 2.1933 89.6 0.665 1.9 3.5
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 4JPK 2.16 46.448 1.34 52503 2606 92.54 0.1906 0.1894 0.1935 0.2143 0.2167
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 13.986 f_angle_d 0.782 f_chiral_restr 0.051 f_bond_d 0.006 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4512 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 46
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing