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1.9 Angstrom Crystal Structure of Superantigen-like Protein, Exotoxin from Staphylococcus aureus, in Complex with Sialyl-LewisX.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3URY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 Protein: 6.6 mg/ml, 0.25 M Sodium chloride, 0.01 M Tris-HCL buffer pH(8.3), 2.4mM LewisX, 5mM BME; Screen: JCSG+ (G6), 0.24M Sodium malonate (pH 7.0), 20%(w/v) PEG 3350., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.28 45.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.983 α = 90 b = 88.904 β = 90 c = 153.839 γ = 90
Symmetry Space Group P 21 21 21
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 225 mm CCD beryllium lenses 2014-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.9 30 99.7 0.065 0.065 26.1 7.1 37801 37801 -3 30.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 100 0.459 0.459 3.9 6.2 1815
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3URY 1.9 29.1 35792 35792 1887 99.71 0.17389 0.17389 0.17174 0.21447 0.2363 RANDOM 37.692
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] -0.18 -0.53 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.285 r_dihedral_angle_4_deg 16.446 r_dihedral_angle_3_deg 10.137 r_long_range_B_refined 8.193 r_long_range_B_other 8.084 r_scangle_other 4.199 r_dihedral_angle_1_deg 3.204 r_mcangle_it 2.805 r_mcangle_other 2.804 r_scbond_it 2.646
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.285 r_dihedral_angle_4_deg 16.446 r_dihedral_angle_3_deg 10.137 r_long_range_B_refined 8.193 r_long_range_B_other 8.084 r_scangle_other 4.199 r_dihedral_angle_1_deg 3.204 r_mcangle_it 2.805 r_mcangle_other 2.804 r_scbond_it 2.646 r_scbond_other 2.646 r_mcbond_it 1.914 r_mcbond_other 1.913 r_angle_refined_deg 1.529 r_angle_other_deg 0.683 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3128 Nucleic Acid Atoms Solvent Atoms 465 Heterogen Atoms 115
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling