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Fab structure of a neutralizing antibody L1 from an early subtype A HIV-1 infected patient
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NH7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 296 0.17 M (NH4)2SO4, 0.085 M cacodylate pH 6.5, 25.5% (w/v) polyethylene glycol (PEG) 8000, and 15% (v/v) glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.58 52.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.101 α = 90 b = 57.463 β = 112.78 c = 60.038 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 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 1.7 41.5 95.8 52788 50571
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 1.7 1.73 81.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 3NH7 1.7 41.5 1.36 52817 50557 2567 95.72 0.1877 0.1865 0.2091 0.2099 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] 1.1969 -4.3672 -4.9677 3.7708
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.492 f_angle_d 1.114 f_chiral_restr 0.073 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3296 Nucleic Acid Atoms Solvent Atoms 532 Heterogen Atoms 6
Software Software Software Name Purpose Blu-Ice data collection MOLREP phasing PHENIX refinement HKL-2000 data reduction SCALEPACK data scaling