☰ Navigation Tabs
Structure of the carbohydrate recognition domain of Dectin-2 complexed with a mammalian-type high mannose Man9GlcNAc2 oligosaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZRV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 295 Drop size:
0.9:0.9 micro-liter of protein:reservoir
protein solution:
2 mg/ml CRD, 5 mM CaCl2, 10 mM Tris-Cl, pH 8.0, 25 mM NaCl, and 2 mM Man9GlcNAc2.
The reservoir solution:
1.0 M NaCl, 6% polyethylene glycol 400 and 0.1 M Tris-Cl, pH 8.0.
freezing solution:
30% polyethylene glycol 400, 1.0 M NaCl, 0.1 M Tris-Cl, pH 8.0, and 2 mM Man9GlcNAc2.
Crystal Properties Matthews coefficient Solvent content 2.85 56.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.055 α = 90 b = 78.834 β = 90 c = 76.459 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS PILATUS 6M 2017-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.39 38.23 99.4 0.08 0.088 0.038 0.99 12.4 5.2 7880 37.47
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.39 2.48 97.3 0.432 0.482 0.207 0.931 5.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 MOLECULAR REPLACEMENT FREE R-VALUE 4ZRV 2.4 38.229 7793 390 99.32 0.2069 0.2052 0.2088 0.2404 0.2407 45.7093
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 12.535 f_angle_d 0.528 f_chiral_restr 0.039 f_bond_d 0.007 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1162 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 88
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing