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Crystal structure of ligand-free VRC03 antigen-binding fragment.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SE8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M HEPES pH 7.5, 13% PEG 4,000,
10 mM CuCl2, 350 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.89 57.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.185 α = 90 b = 50.804 β = 108.15 c = 71.757 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 CCD MARMOSAIC 300 mm CCD 2011-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1 APS 22-ID
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 1.6 50 88.9 22.12 3.6 65283
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 FREE R-VALUE 3se8 1.6 22.954 1.36 65282 3242 88.88 0.1606 0.1596 0.1648 0.1796 0.183
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 12.682 f_angle_d 0.866 f_chiral_restr 0.056 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3391 Nucleic Acid Atoms Solvent Atoms 626 Heterogen Atoms 30
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing