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Neutron structure of GH1 beta-glucosidase Td2F2 ligand-free form 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-DCl (pD 8.9), Reservoir solution: 0.1M CHES (pD 9.5), 0.912M K/Na tartrate, 5% (w/v) 1-butylpyridinium chloride, 0.2M Li2SO4 in heavy water
Crystal Properties Matthews coefficient Solvent content 2.37 48.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.72 α = 90 b = 71.03 β = 90 c = 97.29 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 2021-10-20 M SINGLE WAVELENGTH 2 1 neutron 293 DIFFRACTOMETER iBIX 2021-06-29 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 2.28-6.19 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 1.19 44.3 99.6 0.079 0.033 0.998 11.4 6.6 154133 -3 -3 2 1.8 22.15 99.1 0.25 0.093 0.983 8.6 8 45104 -3 -3
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 1.19 1.21 0.829 0.347 0.755 6.4 2 1.8 1.86 0.972 0.41 0.466 1.7 6.3
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 1.19 44.3 154041 7694 99.5 0.1532 0.1524 0.1488 0.1676 0.173 Random selection 22.95 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 1.8 22.15 45096 2256 99.23 0.1504 0.1492 0.1732 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 14.077 f_angle_d 1.003 f_chiral_restr 0.082 f_plane_restr 0.013 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3458 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 13