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Structure of the catalytic domain of Streptococcus mutans GtfB in tetragonal space group P4322
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AIC Apo subunit A used to generate a model with GtfB sequence.
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
Crystal Properties Matthews coefficient Solvent content 4.37 71.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.13 α = 90 b = 150.13 β = 90 c = 302.783 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 86.92 100 0.314 0.322 0.072 0.996 9.3 20.1 119867
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 99.8 0.882 0.439 21
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 2.5 75.7 113679 6059 99.96 0.21363 0.21216 0.2156 0.24086 0.2429 RANDOM 54.917
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.361 r_dihedral_angle_4_deg 14.964 r_dihedral_angle_3_deg 14.91 r_long_range_B_refined 7.576 r_long_range_B_other 7.555 r_dihedral_angle_1_deg 7.138 r_scangle_other 5.134 r_mcangle_it 4.875 r_mcangle_other 4.875 r_scbond_it 3.387
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.361 r_dihedral_angle_4_deg 14.964 r_dihedral_angle_3_deg 14.91 r_long_range_B_refined 7.576 r_long_range_B_other 7.555 r_dihedral_angle_1_deg 7.138 r_scangle_other 5.134 r_mcangle_it 4.875 r_mcangle_other 4.875 r_scbond_it 3.387 r_scbond_other 3.213 r_mcbond_it 3.193 r_mcbond_other 3.193 r_angle_refined_deg 1.299 r_angle_other_deg 1.201 r_chiral_restr 0.052 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 13133 Nucleic Acid Atoms Solvent Atoms 366 Heterogen Atoms 175
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing