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Crystal structure of the SrpA adhesin from Streptococcus sanguinis with a sialyl galactose disaccharide bound
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 100 mM Na cacodylate, 0.2 M Ca(CH3CO2)2, 18% PEG 8000. SrpA protein was concentrated to 16 mg/mL in 20 mM Tris pH 7.2, 10 mM disaccharide
Crystal Properties Matthews coefficient Solvent content 2.96 58.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 174.62 α = 90 b = 47.005 β = 102.15 c = 64.026 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 MARMOSAIC 300 mm CCD 2015-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.979 APS 21-ID-G
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 50 94.7 0.131 0.142 0.054 7.7 6.8 32930 24.27
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 78 0.5 0.551 0.224 0.881 5.3 1351
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION FREE R-VALUE 2 28.229 1.36 32864 1643 94.37 0.2001 0.1979 0.2025 0.2429 0.244 35.55
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.864 f_angle_d 0.979 f_chiral_restr 0.042 f_bond_d 0.026 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3028 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 54
Software Software Software Name Purpose HKL-2000 data collection HKL-2000 data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction