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Crystal structure of Fab PCT64_LMCA (SAR), the least mutated common ancestor of the HIV-1 broadly neutralizing antibody lineage PCT64
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FEH 5FEH, 1NGZ experimental model PDB 1NGZ 5FEH, 1NGZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.1 M Tris (pH 8), 1 M lithium chloride, 10% w/v PEG 6000, cryoprotected with 30% glycerol
Crystal Properties Matthews coefficient Solvent content 2.67 53.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.199 α = 90 b = 87.158 β = 90 c = 142.565 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 PILATUS3 6M 2016-01-20 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 Sym 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 2.7 50 93.4 0.12 12.4 5.9 27556
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.75 0.47 0.91 998
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 5FEH, 1NGZ 2.702 43.579 1.34 27451 1340 93.4 0.2429 0.2415 0.2416 0.2683 0.2676
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 18.663 f_angle_d 0.487 f_chiral_restr 0.042 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6769 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 10
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing