☰ Navigation Tabs
The structure of the Streptococcus gordonii surface protein SspB in complex with TEV peptide provides clues to the adherence of oral streptococcal adherence to salivary agglutinin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Q2K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20-25% PEG 8000, 0.1M succinic acid,
pH 5.0-5.5, 100mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.45 49.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.223 α = 90 b = 47.695 β = 113.6 c = 64.652 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 200K Osmic Mirrors 2017-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.8 50 98.9 0.084 0.097 0.047 11.8 3.3 31075 17.4
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 1.8 1.83 83.9 0.419 0.567 0.38 0.714 1.6 1.5
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 6Q2K 1.8 37.15 29507 1554 98.81 0.197 0.195 0.1978 0.232 0.2348 RANDOM 22.5
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 -0.08 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.396 r_dihedral_angle_4_deg 15.989 r_dihedral_angle_3_deg 12.415 r_dihedral_angle_1_deg 6.762 r_angle_refined_deg 1.299 r_angle_other_deg 0.882 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.396 r_dihedral_angle_4_deg 15.989 r_dihedral_angle_3_deg 12.415 r_dihedral_angle_1_deg 6.762 r_angle_refined_deg 1.299 r_angle_other_deg 0.882 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2345 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 7
Software Software Software Name Purpose HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction