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Crystal Structure of Superantigen-like Protein, Exotoxin SACOL0473 from Staphylococcus aureus subsp. aureus COL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QEJ PDB entry 2QEJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 295 protein at 7.3 mg/ml 0.25 NaCl, 0.01 M Tris pH 8.3
screen:Classics II, H1, 0.2M MgCl, 0.1M Tris pH 8.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.2 44.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.614 α = 90 b = 62.614 β = 90 c = 129.075 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 CCD MARMOSAIC 300 mm CCD Mirrors 2011-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97917 APS 21-ID-D
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 2.3 56.33 99.6 0.096 26.1 6.5 12065 12065 -3 36.2
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) 2.3 2.34 94.6 0.444 2.5 3.5 565
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 (All) 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 entry 2QEJ 2.3 45 11358 570 99.07 0.1923 0.1923 0.18926 0.187 0.25482 0.2332 RANDOM 26.949
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 r_dihedral_angle_2_deg 32.082 r_dihedral_angle_3_deg 12.274 r_dihedral_angle_4_deg 11.68 r_scangle_it 5.96 r_scbond_it 3.774 r_dihedral_angle_1_deg 3.04 r_mcangle_it 2.413 r_angle_refined_deg 1.918 r_mcbond_it 1.264 r_angle_other_deg 0.922
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.082 r_dihedral_angle_3_deg 12.274 r_dihedral_angle_4_deg 11.68 r_scangle_it 5.96 r_scbond_it 3.774 r_dihedral_angle_1_deg 3.04 r_mcangle_it 2.413 r_angle_refined_deg 1.918 r_mcbond_it 1.264 r_angle_other_deg 0.922 r_mcbond_other 0.338 r_chiral_restr 0.124 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1585 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms
Software Software Software Name Purpose Blu-Ice data collection BALBES phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling