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Crystal structure of the HIV-1 neutralizing antibody 4E10 Fab fragment in complex with a hydrocarbon-stapled peptide containing the 4e10 epitope on gp41.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FX7 PDB ENTRY 2FX7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 295 Reservoir solution: 0.2 M NaCl, 0.1 M Na/K Phosphate pH 6.2, 50% PEG 200, VAPOR DIFFUSION, SITTING DROP, temperature 22K, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.12 60.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 226.107 α = 90 b = 226.107 β = 90 c = 41.824 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD MARMOSAIC 300 mm CCD K-B pair of biomorph mirrors for vertical and horizontal focusing 2010-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0000 APS 23-ID-D
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 2.91 48.95 95.6 0.182 16.4 21.9 14400 13767 -3 63.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.91 2.96 70.4 0.666 3.1 7.8 501
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 PDB ENTRY 2FX7 2.912 48.95 1.34 14389 13737 688 95.47 0.2128 0.2099 0.2096 0.2681 0.2667 RANDOM 69
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] -12.8238 -12.8238 25.6475
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.269 f_angle_d 0.793 f_chiral_restr 0.05 f_bond_d 0.006 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3485 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 19
Software Software Software Name Purpose PHASER phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling