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Crystal structure of NAD-dependent glycoside hydrolase from Flavobacterium sp. (strain K172) in complex with co-factor NAD+ and sulfoquinovose (SQ)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-A0A7D7VZ79-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 100 mM bis-tris propane pH 7, 0.02 mM sodium and potassium phosphate, 28% (w/v) PEG3350, 5 mM NAD+ and 1 mM manganese chloride. SQ powder soaked into the well directly for around 2 minutes
Crystal Properties Matthews coefficient Solvent content 2.42 49.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.517 α = 90 b = 160.381 β = 90 c = 185.749 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 DECTRIS EIGER2 XE 16M 2023-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 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 2.3 51.19 100 0.288 0.299 0.08 0.995 6.2 13.8 73391
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 2.3 2.35 100 1.616 1.675 0.438 0.876 14.4
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 (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 THROUGHOUT 2.3 49.06 69673 3609 99.86 0.19748 0.19499 0.2049 0.24593 0.1998 RANDOM 29.867
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] -0.08 -3.47 3.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.504 r_dihedral_angle_2_deg 12.194 r_long_range_B_refined 7.138 r_long_range_B_other 7.138 r_dihedral_angle_1_deg 7.023 r_scangle_other 5.966 r_mcangle_it 4.298 r_mcangle_other 4.298 r_scbond_it 3.832 r_scbond_other 3.831
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.504 r_dihedral_angle_2_deg 12.194 r_long_range_B_refined 7.138 r_long_range_B_other 7.138 r_dihedral_angle_1_deg 7.023 r_scangle_other 5.966 r_mcangle_it 4.298 r_mcangle_other 4.298 r_scbond_it 3.832 r_scbond_other 3.831 r_mcbond_it 2.875 r_mcbond_other 2.874 r_angle_refined_deg 1.428 r_angle_other_deg 0.484 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11072 Nucleic Acid Atoms Solvent Atoms 740 Heterogen Atoms 284
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing