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Crystal Structure of the HIV-1 BG505 SOSIP.664 Env Trimer Ectodomain, Comprising Atomic-Level Definition of Pre-Fusion gp120 and gp41, in Complex with Human Antibodies PGT122 and 35O22
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JY5 4JY5,4TOY,4J6R experimental model PDB 4TOY 4JY5,4TOY,4J6R experimental model PDB 4J6R 4JY5,4TOY,4J6R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 16% isopropanol, 5.32% PEG1500, 0.2M LiSO4, 0.1M Sodium acetate pH 5.5
Crystal Properties Matthews coefficient Solvent content 4.45 72.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.89 α = 90 b = 128.89 β = 90 c = 313.42 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 CCD RAYONIX MX300HS 2014-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.1 50 73.4 11.3 3.8 39567
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.21 27.8 1.11 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 MOLECULAR REPLACEMENT FREE R-VALUE 4JY5,4TOY,4J6R 3.1 40.739 1.38 29353 1449 55.04 0.2152 0.2135 0.2172 0.248 0.2467
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 8.717 f_angle_d 0.575 f_chiral_restr 0.023 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11344 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 807
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling PHASER phasing