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GH146 beta-L-arabinofuranosidase from Bacteroides thetaioatomicron in complex with beta-l-arabinofurano cyclophellitol aziridine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YQH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 15-17% PEG 3350, MES pH 6.25-6.5, 0.2M ammonium formate, seeding from similar conditions
Crystal Properties Matthews coefficient Solvent content 2.49 50.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.84 α = 90 b = 98.549 β = 90 c = 196.584 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 100 PIXEL DECTRIS EIGER X 16M 2023-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97623 Diamond I03
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 2.4 55.9 100 0.101 0.109 0.041 0.994 16.8 13.7 72064
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 2.4 2.45 1.138 1.237 0.481 0.83 12.7
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 MOLECULAR REPLACEMENT THROUGHOUT 2.4 55.899 71982 3622 99.963 0.191 0.1896 0.1897 0.2208 0.221 61.794
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] 3.914 -1.045 -2.868
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.086 r_dihedral_angle_3_deg 13.437 r_dihedral_angle_1_deg 7.085 r_dihedral_angle_2_deg 6.964 r_lrange_it 6.057 r_lrange_other 6.052 r_scangle_it 3.742 r_scangle_other 3.741 r_mcangle_it 3.134 r_mcangle_other 3.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.086 r_dihedral_angle_3_deg 13.437 r_dihedral_angle_1_deg 7.085 r_dihedral_angle_2_deg 6.964 r_lrange_it 6.057 r_lrange_other 6.052 r_scangle_it 3.742 r_scangle_other 3.741 r_mcangle_it 3.134 r_mcangle_other 3.134 r_scbond_it 2.31 r_scbond_other 2.309 r_mcbond_it 2.016 r_mcbond_other 2.016 r_angle_refined_deg 1.259 r_angle_other_deg 0.492 r_nbd_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.18 r_nbtor_refined 0.163 r_symmetry_nbd_other 0.153 r_symmetry_nbd_refined 0.148 r_nbd_other 0.144 r_metal_ion_refined 0.134 r_xyhbond_nbd_refined 0.114 r_symmetry_nbtor_other 0.067 r_ncsr_local_group_1 0.064 r_chiral_restr 0.062 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12421 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement REFMAC refinement DIALS data collection Aimless data scaling MOLREP phasing DIALS data reduction