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Crystal Structure of a Stabilized DS-SOSIP.mut4 BG505 gp140 HIV-1 Env Trimer, Containing Mutations I201C-P433C (DS), L154M, N300M, N302M, T320L in Complex with Human Antibodies PGT122 and 35O22 at 4.1 Angstrom
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 4.6 293 10.5% PEG 4000, 0.2M AmSO4, 0.1M NaoAc pH 4.6
Crystal Properties Matthews coefficient Solvent content 4.54 72.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.447 α = 90 b = 131.447 β = 90 c = 312.348 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 MX300HE 2016-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 3.4 50 61 0.149 0.158 0.053 5.5 7.8 25676 86.58
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.4 3.52 17.4 1.136 1.305 0.618 0.345 2.5
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 3.412 41.481 1.38 24010 1269 57.96 0.2437 0.2412 0.2446 0.2882 0.2896
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 15.492 f_angle_d 0.861 f_chiral_restr 0.049 f_plane_restr 0.005 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11285 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 735
Software Software Software Name Purpose PHENIX refinement HKL-2000 data collection PHASER phasing PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling DENZO data reduction SCALEPACK data scaling