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Crystal structure of PCDN-38B, a broadly neutralizing anti-HIV antibody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BZD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 277.15 1.6 M sodium dihydrogen phosphate, 0.4 M dipotassium hydrogen phosphate, 0.1 M phosphate-citrate
Crystal Properties Matthews coefficient Solvent content 3.16 61.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.696 α = 90 b = 68.065 β = 96.646 c = 77.937 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 PIXEL DECTRIS EIGER X 16M 2019-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03309 APS 23-ID-B
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 2.08 50 99.1 0.1 1 9 3.5 36353 36.55
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.08 2.2 96.8 0.98 0.7 1.2 3.6
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 5BZD 2.08 45.5 1.35 36304 1878 99.1 0.1923 0.1908 0.191 0.2191 0.2209 42.61
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 18.2059 f_angle_d 0.5781 f_chiral_restr 0.0449 f_plane_restr 0.0047 f_bond_d 0.0025
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3415 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 150
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing