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Crystal structure of beta-glucosidase from Bacteroides ovatus bound to beta-D-Glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold A0AAN3A6K2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 9.5 294 0.1 M CHES buffer, pH 9.5, 30% PEG8000
Full-grown soaked in crystallization drop containing approx 0.1 M Dextrose for 30 min
Crystal Properties Matthews coefficient Solvent content 2.07 40.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.833 α = 72.856 b = 74.965 β = 67.761 c = 87.009 γ = 64.84
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD Mirrors 2025-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.978930 RRCAT INDUS-2 PX-BL21
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 1.95 47.61 97.3 0.155 0.172 0.073 0.983 9.7 5.6 102129 15.23
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 1.95 1.95 96.3 0.676 0.745 0.313 0.802 2.6 5.6
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 1.95 38.67 1.97 102066 5289 97.27 0.2036 0.2017 0.2016 0.2366 0.2363 16.91
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 15.0748 f_angle_d 0.6985 f_chiral_restr 0.0482 f_plane_restr 0.0057 f_bond_d 0.0036
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11534 Nucleic Acid Atoms Solvent Atoms 1223 Heterogen Atoms 26
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing Coot model building PHENIX refinement