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Crystal structure of BG505 SOSIP.v4.1-GT1.2 trimer in complex with gl-PGV20 and PGT124 Fabs
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5W6D PDB entry 5W6D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 0.2 M ammonium sulfate, 0.1 M Tris, pH 8.5, 12% w/v PEG8000
Crystal Properties Matthews coefficient Solvent content 3.58 65.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.057 α = 90 b = 157.666 β = 102.973 c = 158.558 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M 2017-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.0332 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.8 49.76 95.7 0.78 4.3 2.9 63948 104.91
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.82 3.88 0.31
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 PDB entry 5W6D 3.82 49.76 0.31 63928 3180 94.29 0.2723 0.2707 0.2695 0.3011 0.2991 122.39
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 10.1875 f_angle_d 0.5309 f_chiral_restr 0.0435 f_plane_restr 0.0042 f_bond_d 0.0026
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 33286 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 1124
Software Software Software Name Purpose HKL-2000 data collection PHENIX refinement HKL-2000 data reduction Coot model building PHENIX phasing Aimless data scaling