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Crystal Structure of Broadly Neutralizing Antibody N49P7 in Complex with HIV-1 Clade AE strain 93TH057 gp120 core.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TGT 3TGT, 3TNN experimental model PDB 3TNN 3TGT, 3TNN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 294 10% PEG 5000 MME
12% isopropanol
0.1 M MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.92 57.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.436 α = 90 b = 63.867 β = 90 c = 255.285 γ = 90
Symmetry Space Group P 21 21 21
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 300K RH coated flat mirror 2017-05-31 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 2.69 44.261 80.6 0.131 9.3 3.1 23639
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 2.69 2.74 72.2 0.749 1.07 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 3TGT, 3TNN 2.7 44.261 1.38 18015 919 63.11 0.228 0.2248 0.2257 0.2847 0.2838 Random selection
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.46 f_angle_d 1.163 f_chiral_restr 0.076 f_bond_d 0.014 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5822 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 170
Software Software Software Name Purpose PHENIX refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing