☰ Navigation Tabs
Crystal structure of the cleavage-independent prefusion HIV Env glycoprotein trimer of the clade A BG505 isolate (NFL construct) in complex with Fabs PGT122 and PGV19 at 3.39 A
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, SITTING DROP 293.15 0.1M HEPES (pH 7.0), 15% (w/v) PEG4000, and cryo-protected with 25% glycerol
Crystal Properties Matthews coefficient Solvent content 5.32 76.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.247 α = 90 b = 161.247 β = 90 c = 245.651 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 293 PIXEL DECTRIS PILATUS3 6M 2015-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.03321 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3.39 50 98.7 0.206 0.145 0.715 6.9 6.4 49063 91.86
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.39 3.51 99.9 0.559 0.202 1.3 6.1
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 3.4 48.854 1.33 48932 2456 98.5 0.3358 0.3352 0.3376 0.3464 0.3451
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 13.428 f_angle_d 1.726 f_chiral_restr 0.186 f_plane_restr 0.018 f_bond_d 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10823 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 966
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing