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Crystal structure of a HIV-1 clade C isolate Du172.17 HR1.R4.664 Env trimer in complex with human Fabs PGT124 and 35O22
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CEZ PDB entries 5CEZ, 4TOY, 4R26 experimental model PDB 4TOY PDB entries 5CEZ, 4TOY, 4R26 experimental model PDB 4R26 PDB entries 5CEZ, 4TOY, 4R26
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.1M Tris pH=8.4, 25%(v/v) PEG400
Crystal Properties Matthews coefficient Solvent content 4.39 72.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.016 α = 90 b = 127.016 β = 90 c = 316.538 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 PILATUS3 6M 2019-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 97.6 0.85 8.6 6.4 38788 92.5907504709
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.4 3.46 0.45
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 PDB entries 5CEZ, 4TOY, 4R26 3.39228580771 49.5301719699 1.33790597134 38200 1917 95.7753541432 0.244439177019 0.241970008729 0.2433 0.29172476334 0.2903 113.176596028
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 13.312812868 f_angle_d 1.48301479719 f_chiral_restr 0.118800754756 f_bond_d 0.00409734705206 f_plane_restr 0.0038837308944
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11318 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 715
Software Software Software Name Purpose PHENIX refinement PHASER phasing Coot model building HKL-2000 data scaling HKL-2000 data reduction