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Crystal structure of the B41 SOSIP.664 Env trimer with PGT124 and 35O22 Fabs, in P23 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4R26 4R26, 5CEZ experimental model PDB 5CEZ 4R26, 5CEZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 0.1M HEPES (pH 7.0),
8% PEG8000
Crystal Properties Matthews coefficient Solvent content 4.86 74.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 212.326 α = 90 b = 212.326 β = 90 c = 212.326 γ = 90
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 PILATUS 6M 2016-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.03315 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.5 50.046 100 0.1 0.84 10.1 37.5 39580
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 3.5 3.6 100 0.39 1 30.6
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 4R26, 5CEZ 3.526 50.046 1.33 39463 1951 99.7 0.307 0.3061 0.3197 0.3223 0.3343
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 15.855 f_angle_d 0.909 f_chiral_restr 0.056 f_plane_restr 0.015 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11417 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 851
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling HKL-2000 data scaling PHENIX model building HKL-2000 data reduction PHASER phasing