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1.75 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 4RCO PDB-4RCO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 292 Protein: 6.1 mg/ml, 0.5M Sodium chloride, 0.01M Tris-HCL (pH 8.3), 2mM Sialyl-LewisX;Screen: JCSG+ (A3), 0.18M tri-Ammonium citrate, 20% (w/v) PEG3350.
Crystal Properties Matthews coefficient Solvent content 1.56 21.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.975 α = 90 b = 166.881 β = 90 c = 34.144 γ = 90
Symmetry Space Group P 21 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 CCD MARMOSAIC 300 mm CCD C(111) 2014-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 1.75 30 100 0.091 0.091 19.5 7.3 50461 -3 19.9
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 1.75 1.78 100 0.622 3.1 7
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 PDB-4RCO 1.75 29.94 47830 2563 99.62 0.16287 0.16083 0.1702 0.20177 0.2097 RANDOM 22.845
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] -0.09 0.83 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.751 r_dihedral_angle_4_deg 22.144 r_dihedral_angle_3_deg 10.282 r_long_range_B_refined 6.644 r_long_range_B_other 6.249 r_dihedral_angle_1_deg 3.706 r_scangle_other 2.666 r_mcangle_it 1.676 r_mcangle_other 1.676 r_scbond_it 1.657
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.751 r_dihedral_angle_4_deg 22.144 r_dihedral_angle_3_deg 10.282 r_long_range_B_refined 6.644 r_long_range_B_other 6.249 r_dihedral_angle_1_deg 3.706 r_scangle_other 2.666 r_mcangle_it 1.676 r_mcangle_other 1.676 r_scbond_it 1.657 r_scbond_other 1.656 r_angle_refined_deg 1.546 r_mcbond_it 1.044 r_mcbond_other 1.043 r_angle_other_deg 0.817 r_chiral_restr 0.098 r_gen_planes_refined 0.022 r_gen_planes_other 0.018 r_bond_refined_d 0.01 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3182 Nucleic Acid Atoms Solvent Atoms 641 Heterogen Atoms 163
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing