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Crystal Structure of Tier 2 Neutralizing Antibody DH428 from a Rhesus Macaque
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QHL separated Fv and Fc regions of I3.2 Fab from PDB Entry 4QHL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 40% PEG 400 and 100 mM sodium citrate, pH 5.0
Crystal Properties Matthews coefficient Solvent content 3.08 60.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.106 α = 90 b = 74.628 β = 90 c = 102.62 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 PIXEL DECTRIS PILATUS 6M-F 2015-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97916 APS 24-ID-C
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 2.32 60.36 91.72 0.086 13.43 4 22905
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 2.32 2.4 95 0.744 2.2 3.9
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 separated Fv and Fc regions of I3.2 Fab from PDB Entry 4QHL 2.32 60.356 1.35 22892 1213 91.67 0.2204 0.2181 0.2267 0.2646 0.2713 48.6
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 14.497 f_angle_d 1.278 f_chiral_restr 0.082 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3142 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction Coot model building XSCALE data scaling XDS data reduction PHASER phasing