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Crystal Structure of Leukotoxin (LukE) from Staphylococcus aureus subsp. aureus COL.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T5R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 295 Protein: 7mG/mL, 0.25M Sodium chloride, 0.01M Tris, pH 8.3. Screen: JCSG+, D7, 0.2M Lithium sulfate, 0.1M Tris, pH 8.5, 40% v/v PEG 400. VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.9 68.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.904 α = 90 b = 133.904 β = 90 c = 64.473 γ = 90
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 Beryllium lenses 2011-03-31 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) 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 3.2 30 100 0.077 25.8 7.5 9573 9573 -3 87.7
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 3.2 3.26 100 0.552 4 7.6 467
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1T5R 3.2 29.94 9098 9098 459 99.94 0.18055 0.18055 0.17845 0.1823 0.22418 0.2269 RANDOM 107.369
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.219 r_dihedral_angle_4_deg 8.218 r_dihedral_angle_3_deg 7.279 r_scangle_it 3.54 r_scbond_it 2.122 r_mcangle_it 1.573 r_dihedral_angle_1_deg 1.569 r_angle_refined_deg 1.358 r_mcbond_it 0.805 r_angle_other_deg 0.741
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.219 r_dihedral_angle_4_deg 8.218 r_dihedral_angle_3_deg 7.279 r_scangle_it 3.54 r_scbond_it 2.122 r_mcangle_it 1.573 r_dihedral_angle_1_deg 1.569 r_angle_refined_deg 1.358 r_mcbond_it 0.805 r_angle_other_deg 0.741 r_mcbond_other 0.122 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2248 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 12
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling