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Structure of full-length Streptococcus mutans GtfD active site mutant (D465A, D584A) in complex with sucrose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9O9P The search model is also an active site mutant (but serine for aspartate instead of alanine.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 295 Molecular Dimensions condition LMB #44:
24% PEG3350, 2% PEG 400, 0.05M Hepes pH6.8,
0.15M NaCl; apo crystals were soaked with 50mM sucrose (final; 1M stock solution in water)
Crystal Properties Matthews coefficient Solvent content 2.28 46.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.441 α = 90 b = 96.993 β = 90 c = 181.557 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 2022-09-15 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 2.85 83.44 72.8 0.093 0.105 0.047 0.997 9.7 4.2 24970 92.4
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 2.85 3 75.2 1.671 1.885 0.841 0.391 1.1 4.2
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 2.85 75.93 23691 1265 70.98 0.2801 0.27761 0.2775 0.32558 0.3197 RANDOM 96.213
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] 2.93 -6.78 3.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.45 r_dihedral_angle_1_deg 6.507 r_long_range_B_refined 5.861 r_long_range_B_other 5.861 r_mcangle_it 3.681 r_mcangle_other 3.681 r_scangle_other 3.104 r_dihedral_angle_2_deg 2.929 r_mcbond_it 2.158 r_mcbond_other 2.158
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.45 r_dihedral_angle_1_deg 6.507 r_long_range_B_refined 5.861 r_long_range_B_other 5.861 r_mcangle_it 3.681 r_mcangle_other 3.681 r_scangle_other 3.104 r_dihedral_angle_2_deg 2.929 r_mcbond_it 2.158 r_mcbond_other 2.158 r_scbond_it 1.719 r_scbond_other 1.719 r_angle_refined_deg 0.854 r_angle_other_deg 0.351 r_chiral_restr 0.043 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 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 9703 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing