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Crystal Structure at 3.7 A Resolution of Glycosylated HIV-1 Clade A BG505 SOSIP.664 Prefusion Env Trimer with Four Glycans (N197, N276, N362, and N462) removed in Complex with Neutralizing Antibodies 3H+109L and 35O22.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TVP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 4.95% isopropanol, 8.25% PEG 3350, 0.2M ammonium citrate, pH 4.5
Crystal Properties Matthews coefficient Solvent content 4.66 73.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.16 α = 90 b = 131.16 β = 90 c = 315.24 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 MARMOSAIC 300 mm CCD 2016-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.907 41.423 51.3 0.131 3.82 3.1 33547
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3 0.432
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 4TVP 2.907 41.423 1.46 33547 2128 49.92 0.3296 0.3161 0.3195 0.3391 0.3462
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 7.649 f_angle_d 1.632 f_chiral_restr 0.072 f_bond_d 0.013 f_plane_restr 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11480 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 956
Software Software Software Name Purpose PHENIX refinement DENZO data reduction SCALEPACK data scaling PHASER phasing