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Crystal Structure of the RV305 C1-C2 specific ADCC potent antibody DH677.3 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 3TGT 3TGT, 6MFJ experimental model PDB 6MFJ 3TGT, 6MFJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 294 25% PEG 4000
0.1 M MES pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.45 49.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.487 α = 84.82 b = 80.093 β = 82.33 c = 88.688 γ = 82.24
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 2018-03-25 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) 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 50 89.1 0.092 10.2 1.9 30469
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 3.05 90.7 0.442 1.9
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 3TGT, 6MFJ 3 39.6 28977 1492 88.9 0.217 0.214 0.2125 0.274 0.2722 RANDOM 93.95
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] 1.84 1.48 -3.11 -0.25 -1.24 -2.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.977 r_dihedral_angle_3_deg 18.934 r_dihedral_angle_4_deg 17.044 r_long_range_B_other 9.892 r_long_range_B_refined 9.891 r_dihedral_angle_1_deg 6.981 r_scangle_other 4.509 r_mcangle_it 4.161 r_mcangle_other 4.161 r_scbond_other 2.689
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.977 r_dihedral_angle_3_deg 18.934 r_dihedral_angle_4_deg 17.044 r_long_range_B_other 9.892 r_long_range_B_refined 9.891 r_dihedral_angle_1_deg 6.981 r_scangle_other 4.509 r_mcangle_it 4.161 r_mcangle_other 4.161 r_scbond_other 2.689 r_scbond_it 2.688 r_mcbond_it 2.528 r_mcbond_other 2.528 r_angle_refined_deg 1.451 r_angle_other_deg 1.184 r_chiral_restr 0.053 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12342 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 362
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing