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Cystal Structure of Beta-glucuronidase from Bacteroides thetaiotaomicron
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 10%PEG3350, 0.2 M NaCl,0.1 M MES PH 5.5
Crystal Properties Matthews coefficient Solvent content 2.49 50.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.582 α = 90 b = 122.249 β = 90 c = 105.122 γ = 90
Symmetry Space Group C 2 2 21
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 RIGAKU HyPix-6000HE 2021-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-X 2.0
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 23.892 99.57 0.997 12.71 2 44460
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.071 0.866
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION AB INITIO PHASING FREE R-VALUE 2 23.892 44313 2260 99.573 0.192 0.1902 0.1973 0.2322 0.2372 24.639
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] -0.002 -0.005 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.801 r_dihedral_angle_4_deg 18.434 r_dihedral_angle_3_deg 16.445 r_dihedral_angle_1_deg 6.815 r_lrange_it 5.532 r_lrange_other 5.532 r_scangle_it 3.564 r_scangle_other 3.563 r_mcangle_it 2.854 r_mcangle_other 2.853
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.801 r_dihedral_angle_4_deg 18.434 r_dihedral_angle_3_deg 16.445 r_dihedral_angle_1_deg 6.815 r_lrange_it 5.532 r_lrange_other 5.532 r_scangle_it 3.564 r_scangle_other 3.563 r_mcangle_it 2.854 r_mcangle_other 2.853 r_scbond_it 2.367 r_scbond_other 2.366 r_mcbond_it 1.958 r_mcbond_other 1.951 r_angle_refined_deg 1.502 r_angle_other_deg 1.399 r_nbd_other 0.228 r_symmetry_nbd_other 0.208 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.173 r_symmetry_nbd_refined 0.139 r_symmetry_xyhbond_nbd_refined 0.136 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4383 Nucleic Acid Atoms Solvent Atoms 452 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing