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Crystal structure of broadly and potently neutralizing antibody VRC23 in complex with HIV-1 gp120
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SE9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 10.5 % PEG 4000, 4 % MPD, 100 mM Tris/HCl, 200 mM CaCl2 , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.62 53.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.044 α = 90 b = 68.692 β = 90 c = 214.534 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 2012-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.64 50 94.8 0.066 0.066 21.8 4.6 113960 108035 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 3SE9 1.64 23.173 1.35 107945 5396 94.57 0.1652 0.1635 0.1664 0.1976 0.2007 Radom
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 13.047 f_angle_d 1.01 f_chiral_restr 0.06 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6015 Nucleic Acid Atoms Solvent Atoms 1020 Heterogen Atoms 210
Software Software Software Name Purpose SERGUI data collection PHASER phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling