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Crystal structure of bovine Fab NC-Cow1 in complex with HIV-1 BG505 SOSIP.664, and human Fabs 35022 and PGT128
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CEZ 5CEZ,4TOY,3TV3, 6OO0 experimental model PDB 4TOY 5CEZ,4TOY,3TV3, 6OO0 experimental model PDB 3TV3 5CEZ,4TOY,3TV3, 6OO0 experimental model PDB 6OO0 5CEZ,4TOY,3TV3, 6OO0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.56 298 0.2M sodium citrate, 0.1M Tris, 30% Peg400
Crystal Properties Matthews coefficient Solvent content 4.46 72.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 215.244 α = 90 b = 215.244 β = 90 c = 438.798 γ = 120
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 S 6M 2018-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) 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 4.08 63.9 100 0.219 0.232 0.076 0.791 11.2 9.2 30902 -3 174
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 4.08 4.17 100 2.15 2.28 0.76 0.34 8.9
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 5CEZ,4TOY,3TV3, 6OO0 4.084 48.755 1.33 30888 1556 98.53 0.3328 0.3322 0.3356 0.3431 0.3442
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 12.629 f_angle_d 0.94 f_chiral_restr 0.051 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10120 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 678
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing