☰ Navigation Tabs
Crystal structure of hinokiresinol synthase in complex with 1,7-bis(4-hydroxyphenyl)hepta-1,6-dien-3-one
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 100mM sodium cacodylate trihydrate (pH6.5), 200mM ammonium sulfate, 20% PEG 8000, 2mM inhibitor
Crystal Properties Matthews coefficient Solvent content 2.2 44.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.831 α = 90 b = 103.831 β = 90 c = 103.831 γ = 90
Symmetry Space Group P 21 3
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 EIGER X 4M 2022-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.1 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.2 46.43 100 0.243 0.998 14.5 22.4 19260 28.51
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 1.234 0.891 3.7
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 2.2 46.43 1.37 19236 1923 99.99 0.1755 0.1708 0.1706 0.219 0.2196 27.97
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 7.0242 f_angle_d 0.8077 f_chiral_restr 0.0532 f_bond_d 0.0056 f_plane_restr 0.0056
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2650 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 27
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing