Navigation Tabs Neutron structure of GH1 beta-glucosidase Td2F2 glucose 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 9.5 293 Protein solution: protein 20mg/mL, 5mM Tris pD 8.9
Reservoir solution: 0.1M CHES pD 9.5, 0.940M K/Na tartrate, 5% (w/v) 1-butylpyridinium chloride, 0.2M Li2SO4, 0.2M glucose in heavy water
Crystal Properties Matthews coefficient Solvent content 2.37 48.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.65 α = 90 b = 71.09 β = 90 c = 97.38 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 2022-05-15 M SINGLE WAVELENGTH 2 1 neutron 293 DIFFRACTOMETER iBIX 2022-04-01 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 1.2 44.3 95.7 0.072 0.03 0.998 14.2 6.7 144269 2 1.7 19.74 98.1 0.224 0.088 0.984 14.2 7.2 52857
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 1.2 1.22 0.885 0.355 0.73 2.2 7 2 1.7 1.76 0.828 0.378 0.428 2.2 5.3
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 1.2 44.3 144184 7202 95.42 0.1533 0.1528 0.1482 0.1622 0.1693 Random selection 23.4 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 1.7 19.74 52854 2634 98.18 0.1495 0.1484 0.1695 Random selection 23.4
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 13.354 f_angle_d 1.21 f_chiral_restr 0.089 f_plane_restr 0.008 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3458 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms 25
