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Germline-targeting HIV-1 gp120 engineered outer domain eODgt8 in complex with Fab eOD-CL02.1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IES experimental model PDB 6WFY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M magnesium nitrate, 20% Peg3350, 15% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.71 54.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.039 α = 90 b = 72.601 β = 107.52 c = 93.817 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS PILATUS 6M 2019-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.7 39.883 98.3 0.158 0.174 0.072 0.988 7.7 5.6 18286 -3 52.94
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 2.7 2.83 99.4 1.04 1.15 0.473 0.753 1.6 5.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.7 39.883 18169 870 97.369 0.277 0.2759 0.273 0.3061 0.2893 53.215
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] 1.514 -4.092 -2.391 2.885
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.729 r_dihedral_angle_3_deg 11.71 r_lrange_it 7.464 r_dihedral_angle_1_deg 5.678 r_dihedral_angle_2_deg 3.833 r_mcangle_it 3.187 r_scangle_it 2.818 r_mcbond_it 1.789 r_scbond_it 1.609 r_angle_refined_deg 1.131
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.729 r_dihedral_angle_3_deg 11.71 r_lrange_it 7.464 r_dihedral_angle_1_deg 5.678 r_dihedral_angle_2_deg 3.833 r_mcangle_it 3.187 r_scangle_it 2.818 r_mcbond_it 1.789 r_scbond_it 1.609 r_angle_refined_deg 1.131 r_nbtor_refined 0.307 r_symmetry_xyhbond_nbd_refined 0.286 r_symmetry_nbd_refined 0.241 r_nbd_refined 0.227 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.068 r_bond_refined_d 0.004 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4430 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing