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Crystal structure of the germline-targeting HIV-1 gp120 engineered outer domain, eOD-GT6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TYG PDB ENTRY 3TYG CHAIN A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 20% w/v PEG3350, 0.2 M magnesium acetate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.38 48.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.96 α = 90 b = 217.73 β = 119.97 c = 44.99 γ = 90
Symmetry Space Group P 1 21 1
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 2012-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03320 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.5 40 99.9 0.142 8.1 3.9 25769 25751
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 99.9 0.43 2.9 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3TYG CHAIN A 2.5 38.97 2 25769 24371 1336 99.71 0.21242 0.20969 0.2979 0.26159 0.3372 RANDOM 19.897
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] -14.11 4.15 34.73 -20.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.201 r_dihedral_angle_3_deg 17.73 r_dihedral_angle_4_deg 15.701 r_dihedral_angle_1_deg 7.278 r_angle_refined_deg 1.154 r_angle_other_deg 0.757 r_chiral_restr 0.07 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.201 r_dihedral_angle_3_deg 17.73 r_dihedral_angle_4_deg 15.701 r_dihedral_angle_1_deg 7.278 r_angle_refined_deg 1.154 r_angle_other_deg 0.757 r_chiral_restr 0.07 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5071 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 112
Software Software Software Name Purpose JBluIce-EPICS data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling