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Crystal Structure of Honey Truffle Active Component 1 through 4 with glucose bound (Monoclinic P form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold 'alphafold'
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 12.5% (v/v) MPD, 12.5% PEG 1000, 12.5% (w/v) PEG 3350, 0.05M Sodium HEPES, 0.05M MOPS pH 7.5, 0.02 M D-Glucose, 0.02 M D-Mannose, 0.02 M D-Galactose, 0.02 M L-Fucose, 0.02 M D-Xylose, 0.02 M N-Acetyl-D-Glucosamine, 0.5 mM Manganese(II) chloride tetrahydrate, 0.5 mM Cobalt chloride hexahydrate, 0.5 mM Nickel chloride hexahydrate, 0.5 mM Zinc acetate dihydrate
Crystal Properties Matthews coefficient Solvent content 2.31 46.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.638 α = 90 b = 44.472 β = 106.68 c = 63.748 γ = 90
Symmetry Space Group P 1 21 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 PIXEL Bruker PHOTON III 2025-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.5418
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 1.7 25.17 99.1 0.053 0.055 0.014 1 28.3 13.8 26884
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 1.7 1.73 96.9 1.566 1.68 0.602 0.767 7.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.7 20.89 1.33 26690 1299 98.27 0.1911 0.1888 0.1998 0.2402 0.2449
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 17.109 f_angle_d 1.019 f_chiral_restr 0.065 f_plane_restr 0.012 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1873 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 13
Software Software Software Name Purpose PHENIX refinement Aimless data scaling SAINT data reduction PHASER phasing PDB_EXTRACT data extraction