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Fab structure of a neutralizing antibody L3 from an early subtype A HIV-1 infected patient
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4F57
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 296 28% PEG 4K, 0.17 M Li2SO4, 0.085 M Tris pH 8.5, and 15% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.97 58.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.403 α = 90 b = 126.413 β = 90.08 c = 120.082 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE MAR scanner 300 mm plate 2011-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.03319 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.488 46.5 99.8 75889 76041
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.488 2.54 99
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 4F57 2.488 46.5 1.35 76841 75512 3776 98.27 0.2105 0.208 0.2044 0.2564 0.2512 random
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] -7.082 0.3747 -6.7244 13.8064
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.188 f_angle_d 1.165 f_chiral_restr 0.078 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13078 Nucleic Acid Atoms Solvent Atoms 682 Heterogen Atoms 75
Software Software Software Name Purpose Blu-Ice data collection MOLREP phasing PHENIX refinement HKL-2000 data reduction SCALEPACK data scaling