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Crystal structure of the neutralizing HIV antibody 2F5 Fab fragment (recombinantly produced Fab) with 11 aa gp41 MPER-derived peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TJH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.6 298 20% isopropanol, 20% PEG 4000, 0.1 M Na citrate pH 5.6. 0.5 uL protein + 0.35 uL drop., VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.29 62.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.505 α = 90 b = 64.976 β = 90 c = 173.046 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 CCD MARMOSAIC 300 mm CCD 2009-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
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 2.6 43.5 100 0.094 10.8 7.2 21061 21061 2 2
Refinement Statistics Diffraction ID Structure Solution 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 1TJH 2.6 43.478 0.37 20983 1990 99.81 0.1946 0.1902 0.1847 0.2356 0.229
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] 1.4905 4.0835 -5.574
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.3 f_angle_d 1.365 f_chiral_restr 0.121 f_bond_d 0.026 f_plane_restr 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3477 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms
Software Software Software Name Purpose PHENIX model building PHENIX refinement d*TREK data reduction d*TREK data scaling PHENIX phasing