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Structure of the catalytic domain of Streptococcus mutans GtfB complexed to acarbose in tetragonal space group P4322
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8FJ9 PDB ID 8FJ9 is the corresponding apo structure in tetragonal space group P4322.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 295 2 M ammonium sulfate, 0.1 M Bis-Tris; tetragonal apo crystals were soaked with acarbose at a 1:10 molar ratio for 5-10 mins (stock solution of 100 mM in water; final concentration 1-2 mM)
Crystal Properties Matthews coefficient Solvent content 4.34 71.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.546 α = 90 b = 149.546 β = 90 c = 303.085 γ = 90
Symmetry Space Group P 43 2 2
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 S 16M 2019-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
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 2.5 86.72 100 0.252 0.266 0.084 0.99 9.3 10.2 119150 41.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 100 0.595 0.446 1.8 10.8
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 THROUGHOUT 2.5 83.715 1.35 119032 6016 99.92 0.188 0.1859 0.1882 0.2279 0.2266
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 6.731 f_angle_d 1.241 f_chiral_restr 0.064 f_bond_d 0.011 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13226 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 377
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing