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Crystal structure of the broadly neutralizing antibody N49P6 Fab in complex with HIV-1 Clade A/E strain 93TH057 gp120 core.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6BCK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 294 15% PEG 3350
0.1 M Tris-HCl pH 8.0
Crystal Properties Matthews coefficient Solvent content 3 58.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.436 α = 90 b = 80.815 β = 90 c = 195.214 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 6M 2017-11-16 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) 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 2.55 50 92 0.276 0.166 0.99 6.4 3.1 31853 40.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.59 89.3 0.727 0.556 0.56 1.1 2.2
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6BCK 2.55 34.327 1.33 31820 1599 91.69 0.2212 0.2185 0.2202 0.2733 0.2748
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 9.35 f_angle_d 1.291 f_chiral_restr 0.07 f_bond_d 0.011 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5864 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 154
Software Software Software Name Purpose PHENIX refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing