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Crystal structure of the octameric pore complex of the Staphylococcus aureus Bi-component Toxin LukGH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B07 3B07 prepared using CHAINSAW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 Drops consisted of 100 nl protein in 20 mM HEPES buffer pH 7.5 and 100 nl reservoir 30 mM MgCl2, 30 mM CaCl2, 0.1 M Na HEPES/MOPS buffer pH 7.5, 12.5 % v/v MPD, 12.5 % w/v PEG 1000, 12.5 % w/v PEG 3350. Crystals appeared after 7 days.
Crystal Properties Matthews coefficient Solvent content 4.39 71.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.497 α = 90 b = 198.558 β = 103.26 c = 179.535 γ = 90
Symmetry Space Group P 1 21 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 2013-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1.0000 MAX II I911-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.8 48.188 97.9 0.16 0.194 0.109 10.1 3.1 222018 222018 56.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 95.4 0.871 0.871 0.591 0.9 3.1 31557
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 3B07 prepared using CHAINSAW 2.8 48 218497 2207 96 0.2387 0.2381 0.2484 0.2923 0.3025 RANDOM 36.001
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] 4.69 -3.36 -1.99 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.491 r_dihedral_angle_3_deg 20.748 r_dihedral_angle_4_deg 20.721 r_dihedral_angle_1_deg 8.109 r_mcangle_it 3.887 r_scbond_it 2.696 r_mcbond_it 2.318 r_angle_refined_deg 1.796 r_chiral_restr 0.112 r_bond_refined_d 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.491 r_dihedral_angle_3_deg 20.748 r_dihedral_angle_4_deg 20.721 r_dihedral_angle_1_deg 8.109 r_mcangle_it 3.887 r_scbond_it 2.696 r_mcbond_it 2.318 r_angle_refined_deg 1.796 r_chiral_restr 0.112 r_bond_refined_d 0.013 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 37415 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction SCALA data scaling PDB_EXTRACT data extraction PHASER phasing REFMAC refinement XSCALE data reduction