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3.9 Angstrom Crystal Structure of a Fully and Natively Glycosylated BG505 SOSIP.664 HIV-1 Env Trimer in Complex with the Broadly Neutralizing Antibodies IOMA and 10-1074.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TVP 4TVP, 4FQ2, 4TNN, 4XVS experimental model PDB 4FQ2 4TVP, 4FQ2, 4TNN, 4XVS experimental model PDB 4TNN 4TVP, 4FQ2, 4TNN, 4XVS experimental model PDB 4XVS 4TVP, 4FQ2, 4TNN, 4XVS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 200 mM ammonium citrate tribasic pH 7.0
100 mM imidazole pH 7.0
20% PEG MME 2,000
Crystal Properties Matthews coefficient Solvent content 4.23 70.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 217.509 α = 90 b = 217.509 β = 90 c = 156.009 γ = 120
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 2015-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 1.00 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 3.9 80.63 100 0.35 0.08 0.99 7.6 18.2 25079
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.9 4.17 100 2.85 0.68 0.3 1.5 18.3
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 FREE R-VALUE 4TVP, 4FQ2, 4TNN, 4XVS 3.9 80.63 1.96 25058 1276 99.93 0.3004 0.296 0.3223 0.3311 0.3563
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 13.862 f_angle_d 1.108 f_chiral_restr 0.051 f_plane_restr 0.005 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11194 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 1427
Software Software Software Name Purpose PHENIX refinement Coot model building Aimless data scaling iMOSFLM data reduction PHASER phasing