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Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MNV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.2 298 Reservoir: Qiagen AmSO4 suite condition with 2 M ammonium sulfate, 0.2 M ammonium acetate. Drop: 0.5 uL protein + 0.5 uL reservoir., pH 7.2, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.27 45.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.365 α = 90 b = 60.436 β = 91.22 c = 80.118 γ = 90
Symmetry Space Group C 1 2 1
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 225 mm CCD 2009-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM
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 1.8 42.3 96.6 0.073 13.2 7 40173 38807 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 3MNV 1.8 40.05 0.25 38721 1997 96.38 0.1886 0.1869 0.1812 0.2208 0.2152
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] -5.5595 0.8531 6.5605 -1.001
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.112 f_angle_d 1.155 f_chiral_restr 0.081 f_bond_d 0.009 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3323 Nucleic Acid Atoms Solvent Atoms 345 Heterogen Atoms 25
Software Software Software Name Purpose PHENIX model building PHENIX refinement d*TREK data reduction d*TREK data scaling PHENIX phasing