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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 2WD6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 3M Sodium acetate trihydrate, 0.1M Hepes, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.5 50.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.505 α = 90 b = 121.505 β = 90 c = 50.745 γ = 90
Symmetry Space Group P 43 21 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 PILATUS 200K Osmic Mirrors 2014-03-10 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 2 30 97.7 0.118 0.122 0.027 9.9 15.5 25664 27.7
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 2.03 82.8 0.445 0.527 0.275 0.839 2.4 3.1
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 2wd6 2 29.47 24276 1303 97.43 0.1955 0.1935 0.2011 0.2355 0.2391 RANDOM 31.4
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 38.908 r_dihedral_angle_4_deg 20.219 r_dihedral_angle_3_deg 11.69 r_dihedral_angle_1_deg 6.225 r_angle_refined_deg 1.111 r_angle_other_deg 0.837 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.908 r_dihedral_angle_4_deg 20.219 r_dihedral_angle_3_deg 11.69 r_dihedral_angle_1_deg 6.225 r_angle_refined_deg 1.111 r_angle_other_deg 0.837 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2470 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 1
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing