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Structure of langerin CRD with alpha-Me-GlcNAc.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3P5G pdb entry 3P5G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 Protein solution: 2.3-4.0 mg/mL langerin, 2.5 mM CaCl2, 10-100 mM Tris (pH 8.0), 25 mM NaCl and 60mM alpha-Me-GlcNAc. The reservoir solution contained 0.1 M HEPES (pH 7.0), 0.1-0.2 M MgCl2, and 20-35% polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.32 46.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.89 α = 90 b = 79.89 β = 90 c = 90.47 γ = 90
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 ADSC QUANTUM 315r 2011-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.97650 ALS 5.0.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.75 47.92 99.4 0.055 21.8 7.2 56914
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.84 98.8 0.228 7.4 7.1
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) 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 FOURIER SYNTHESIS pdb entry 3P5G 1.75 35.73 56680 2887 99.17 0.1824 0.1797 0.178 0.2333 0.232
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 13.913 f_angle_d 1.125 f_chiral_restr 0.088 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4179 Nucleic Acid Atoms Solvent Atoms 642 Heterogen Atoms 68
Software Software Software Name Purpose BOS data collection PHENIX model building PHENIX refinement MOSFLM data reduction SCALA data scaling PHENIX phasing