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Crystal structure of the ADCC-Potent Antibody N60-I3 Fab in complex with HIV-1 Clade A/E gp120 and M48u1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TNN PDB ENTRY 3TNN FOR N60-I3, PDB ENTRY 4H8W FOR GP120, PDB ENTRY 4JZW FOR M48U1 experimental model PDB 4H8W PDB ENTRY 3TNN FOR N60-I3, PDB ENTRY 4H8W FOR GP120, PDB ENTRY 4JZW FOR M48U1 experimental model PDB 4JZW PDB ENTRY 3TNN FOR N60-I3, PDB ENTRY 4H8W FOR GP120, PDB ENTRY 4JZW FOR M48U1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 294 10-16% PEG 8000, 0.1 M Tris-HCl pH 8.5, 65 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.03 59.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.305 α = 90 b = 102.575 β = 90 c = 108.038 γ = 90
Symmetry Space Group P 21 21 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 CCD MARMOSAIC 325 mm CCD RH coated flat mirror 2013-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.12709 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.2 50 93.7 0.126 10.7 3.8 18694 17516
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.26 96 0.899 1.3 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 3TNN FOR N60-I3, PDB ENTRY 4H8W FOR GP120, PDB ENTRY 4JZW FOR M48U1 3.2 36.013 16589 876 93.76 0.2226 0.21981 0.2208 0.27702 0.2746 RANDOM 116.914
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] 0.98 -8.03 7.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.936 r_dihedral_angle_4_deg 21.557 r_dihedral_angle_3_deg 20.34 r_long_range_B_refined 7.916 r_long_range_B_other 7.916 r_dihedral_angle_1_deg 7.834 r_scangle_other 3.304 r_mcangle_it 3.101 r_mcangle_other 3.072 r_scbond_it 2.226
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.936 r_dihedral_angle_4_deg 21.557 r_dihedral_angle_3_deg 20.34 r_long_range_B_refined 7.916 r_long_range_B_other 7.916 r_dihedral_angle_1_deg 7.834 r_scangle_other 3.304 r_mcangle_it 3.101 r_mcangle_other 3.072 r_scbond_it 2.226 r_scbond_other 1.971 r_mcbond_it 1.813 r_mcbond_other 1.813 r_angle_refined_deg 1.411 r_angle_other_deg 0.836 r_chiral_restr 0.08 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6042 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 126
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling