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Structure of the Fab fragment of N62, a protective monoclonal antibody to the nonreducing end of Francisella tularensis O-antigen
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OZ9 pdb entry 3OZ9 (light chain) and pdb entry 3D9A (heavy chain) experimental model PDB 3D9A pdb entry 3OZ9 (light chain) and pdb entry 3D9A (heavy chain)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 290 Microseeding by mixing 0.5 ul of Fab (12 mg/ml in 20 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.02% NaN3) with 0.5 ul of reservoir solution [0.1 M bistris (pH 6.5), 0.2 M ammonium acetate, 25% w/v PEG 3350] and streaking after equilibration, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.51 50.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.874 α = 90 b = 87.076 β = 90 c = 153.589 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 IMAGE PLATE RIGAKU RAXIS IV 2012-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 2.593 15 98.8 0.068 14.6 3.8 28828 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.69 98.1 0.325 3.7
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) 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 pdb entry 3OZ9 (light chain) and pdb entry 3D9A (heavy chain) 2.59 14.87 28036 1946 96 0.225 0.222 0.2206 0.268 0.2653 36.78
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 10.369 f_angle_d 0.666 f_chiral_restr 0.043 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6220 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 4
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction