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Glucan Binding Protein C of Streptococcus mutans Mediates both Sucrose-Independent and Sucrose-Dependent Adherence
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UQZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.5 295 25% PEG 3350, 0.1M citrate
Crystal Properties Matthews coefficient Solvent content 2.58 52.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 210.02 α = 90 b = 47.94 β = 96.34 c = 40.089 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-300 2017-11-29 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) 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 1.75 46.72 98.5 0.153 0.094 0.99 8.6 3.6 39634 16
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 1.75 1.78 96.5 0.529 0.625 2.7 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5UQZ 1.75 46.72 37660 1972 98.43 0.20834 0.20696 0.2128 0.23474 0.2404 RANDOM 20.26
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] -0.02 0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.887 r_dihedral_angle_3_deg 13.466 r_dihedral_angle_4_deg 10.424 r_dihedral_angle_1_deg 6.581 r_long_range_B_refined 4.042 r_long_range_B_other 3.945 r_scangle_other 1.901 r_angle_refined_deg 1.642 r_mcangle_it 1.592 r_mcangle_other 1.592
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.887 r_dihedral_angle_3_deg 13.466 r_dihedral_angle_4_deg 10.424 r_dihedral_angle_1_deg 6.581 r_long_range_B_refined 4.042 r_long_range_B_other 3.945 r_scangle_other 1.901 r_angle_refined_deg 1.642 r_mcangle_it 1.592 r_mcangle_other 1.592 r_scbond_it 1.168 r_scbond_other 1.168 r_angle_other_deg 0.976 r_mcbond_it 0.917 r_mcbond_other 0.915 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2744 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing