Navigation Tabs Neutron structure of GH1 beta-glucosidase Td2F2 2F-Glc complex at room temperature
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WH5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.9 293 Protein solution: protein reacted 2-deoxy-2-fluoro glucoside 30mg/mL, 5mM Tris pD 8.9
Reservoir solution : 0.1M CHES pD 9.5, 0.890M K/Na tartrate, 5% (w/v) 1-butylpyridinium chloride, 0.2M Li2SO4, in heavy water
Crystal Properties Matthews coefficient Solvent content 2.37 48.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.54 α = 90 b = 71.23 β = 90 c = 97.2 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 PIXEL DECTRIS PILATUS 6M 2023-02-18 M SINGLE WAVELENGTH 2 1 neutron 293 DIFFRACTOMETER iBIX 2023-01-17 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A 2 SPALLATION SOURCE J-PARC MLF BEAMLINE BL-03 1.86-5.76 JPARC MLF BL-03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) 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 1.32 44.29 97.7 0.078 0.032 0.998 13.5 6.6 110952 14 2 1.7 20.07 98.5 0.184 0.071 0.991 2 7.6 53007
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.32 1.34 0.843 0.351 0.746 2.1 6.6 2 1.7 1.76 0.76 0.343 0.556 2 5.5
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 1.32 44.29 1.34 110877 5532 97.46 0.1491 0.1485 0.1482 0.16 0.1602 Random selection 20.44 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 1.7 20.07 53005 2629 98.6 0.1555 0.1548 0.1698 Random selection
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 12.9686 f_angle_d 1.0536 f_chiral_restr 0.0863 f_plane_restr 0.0132 f_bond_d 0.0098
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3458 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms 24
