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Crystal structure of toxic shock syndrome toxin-1 (TSST-1) from Staphylococcus aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TSS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 0.2 M Sodium Chloride, 0.1 M Bis-Tris, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.78 30.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.922 α = 90 b = 40.316 β = 117.3 c = 98.76 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 225 mm CCD 3.0 Undulator 2013-11-06 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) 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 1.28 30 98.8 0.054 21.7 3.7 97363 97363 -3 19.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.28 1.31 97.7 0.57 2.4 3.6
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4TSS 1.28 29.27 87967 87967 4659 98.71 0.14307 0.14122 0.17697 0.1931 RANDOM 19.346
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 -0.2 1.07 -0.64
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 47.196 r_dihedral_angle_2_deg 32.05 r_sphericity_bonded 11.803 r_dihedral_angle_3_deg 9.614 r_dihedral_angle_4_deg 7.687 r_long_range_B_refined 5.273 r_long_range_B_other 4.406 r_dihedral_angle_1_deg 4.104 r_scangle_other 3.572 r_scbond_it 3.158
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 47.196 r_dihedral_angle_2_deg 32.05 r_sphericity_bonded 11.803 r_dihedral_angle_3_deg 9.614 r_dihedral_angle_4_deg 7.687 r_long_range_B_refined 5.273 r_long_range_B_other 4.406 r_dihedral_angle_1_deg 4.104 r_scangle_other 3.572 r_scbond_it 3.158 r_scbond_other 3.111 r_rigid_bond_restr 2.876 r_mcangle_other 2.596 r_mcangle_it 2.59 r_mcbond_it 2.213 r_mcbond_other 2.189 r_angle_refined_deg 1.645 r_angle_other_deg 0.869 r_chiral_restr 0.11 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3102 Nucleic Acid Atoms Solvent Atoms 521 Heterogen Atoms
Software Software Software Name Purpose Blu-Ice data collection BALBES phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling