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Crystal structure of the neutralizing HIV antibody 2F5 Fab fragment (recombinantly produced Fab) with 17 aa gp41 MPER-derived peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TJI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.6 298 Reservoir; Hampton Research Crystal Screen 40 = 20% isopropanol, 20% PEG 4000, 100 mM Na citrate pH 5.6. Drop: 0.5 uL protein + 0.35 uL reservoir. Reservoir was NOT supplemented with 100 mM NaCl as in Ofek et al. 2004., VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.3 62.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.82 α = 90 b = 65.229 β = 90 c = 174.205 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 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 2.3 43.7 100 0.062 15.4 7.3 30678 30678 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 1TJI 2.3 43.683 0.19 30459 1986 99.47 0.1862 0.1839 0.176 0.2193 0.2077
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] 2.4653 0.1352 -2.6005
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.999 f_angle_d 1.348 f_chiral_restr 0.142 f_bond_d 0.027 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3506 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms
Software Software Software Name Purpose PHENIX model building PHENIX refinement d*TREK data reduction d*TREK data scaling PHENIX phasing