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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 1MHH 1MHH, 1TJG experimental model PDB 1TJG 1MHH, 1TJG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 298 Qiagen AmSO4 suite, reservoir: 2.2 M ammonium sulfate, 0.2 M lithium nitrate. Drop: 0.5 uL protein + 0.5 uL reservoir., VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.49 64.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.378 α = 90 b = 158.378 β = 90 c = 92.975 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 CCD MARMOSAIC 225 mm CCD 2009-08-10 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 2.4 45.278 99.2 0.058 11.4 3.2 51941 51525 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 1MHH, 1TJG 2.4 45.278 0.06 51189 1983 98.49 0.1826 0.1808 0.1686 0.2278 0.2158
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 15.407 f_angle_d 1.075 f_chiral_restr 0.072 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6595 Nucleic Acid Atoms Solvent Atoms 417 Heterogen Atoms 51
Software Software Software Name Purpose PHENIX model building PHENIX refinement d*TREK data reduction d*TREK data scaling PHENIX phasing