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Germline-targeting HIV-1 gp120 engineered outer domain eODgt8 in complex with Fab eOD-PL01.1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IES experimental model PDB 7N3H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2M potassium dihydrogen phosphate, 20% Peg3350
Crystal Properties Matthews coefficient Solvent content 3.16 61.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.767 α = 90 b = 166.767 β = 90 c = 100.693 γ = 120
Symmetry Space Group P 64 2 2
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 2019-06-13 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 3.55 38.55 99.4 0.26 0.274 0.087 0.997 9.1 9.5 10327 -3 166
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 3.55 3.89 99.9 3.1 3.25 1 0.613 1 9.9
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 3.55 38.55 9825 447 94.163 0.267 0.2654 0.2692 0.2994 0.3097 162.615
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] 1.112 0.556 1.112 -3.606
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.397 r_dihedral_angle_6_deg 12.382 r_lrange_it 11.897 r_dihedral_angle_1_deg 6.478 r_mcangle_it 5.699 r_scangle_it 5.203 r_dihedral_angle_2_deg 4.068 r_mcbond_it 3.176 r_scbond_it 2.859 r_angle_refined_deg 0.994
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.397 r_dihedral_angle_6_deg 12.382 r_lrange_it 11.897 r_dihedral_angle_1_deg 6.478 r_mcangle_it 5.699 r_scangle_it 5.203 r_dihedral_angle_2_deg 4.068 r_mcbond_it 3.176 r_scbond_it 2.859 r_angle_refined_deg 0.994 r_nbtor_refined 0.303 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.168 r_symmetry_nbd_refined 0.132 r_symmetry_xyhbond_nbd_refined 0.113 r_chiral_restr 0.067 r_gen_planes_refined 0.003 r_bond_refined_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4480 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing