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Structure of langerin CRD I313 D288 complexed with 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 50mM MeGlcNAc.
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 2.28 46.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.55 α = 90 b = 79.55 β = 90 c = 89.88 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 PIXEL PSI PILATUS 6M 2012-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97945 SSRL BL11-1
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 1.85 39.13 99.2 0.036 23.2 3.8 47327 21.47
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.95 98.5 0.232 0.232 3.4 3.8 6843
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 1.85 39.13 47301 2407 99.08 0.172 0.1698 0.1711 0.2139 0.2162 21.7
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 13.481 f_angle_d 1.114 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 4181 Nucleic Acid Atoms Solvent Atoms 544 Heterogen Atoms 69
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction Blu-Ice data collection XDS data reduction PHENIX phasing