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Crystal structure of broadly neutralizing antibody N49P6 Fab in complex with HIV-1 BG505 SOSIP.664 Env trimer ectodomain.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TVP 4TVP, 6BCK experimental model PDB 6BCK 4TVP, 6BCK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 294 12% PEG 3350
0.1 M Tris-HCl pH 8.0
Crystal Properties Matthews coefficient Solvent content 3.16 61.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.703 α = 90 b = 164.703 β = 90 c = 164.703 γ = 90
Symmetry Space Group P 21 3
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 2018-11-09 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) 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 4.05 50 99.6 0.113 0.053 22.8 5.5 12543 175.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 4.05 4.12 99.8 0.757 0.48 1 4.6
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 4TVP, 6BCK 4.05 39.946 1.37 12495 573 99.4 0.2578 0.2546 0.2572 0.3146 0.3128
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 5.941 f_angle_d 1.216 f_chiral_restr 0.067 f_bond_d 0.008 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7725 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 544
Software Software Software Name Purpose PHENIX refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing