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1.7 Angstrom Crystal Structure of leukotoxin LukD from Staphylococcus aureus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PVL pdb entry 1PVL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 Protein: 2.6mG/mL, 0.5M Sodium chloride, 0.01M Tris-HCL buffer, 0.5mM TCEP;
Screen: Classics II (G7), 0.2M Ammonium acetate, 0.1M BIS-TRIS, 25% (w/v) PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.28 46.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.74 α = 90 b = 49.944 β = 90 c = 134.868 γ = 90
Symmetry Space Group P 21 21 21
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 beryllium lenses 2014-04-10 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) 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 1.7 30 99.9 0.067 0.067 22.9 6 37802 37802 -3 23.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 99.9 0.615 0.615 3 5.9 1897
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1PVL 1.7 27.95 35860 35860 1876 99.77 0.16891 0.16747 0.1763 0.19599 0.2056 RANDOM 27.86
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] 1.53 0.78 -2.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.869 r_dihedral_angle_3_deg 10.953 r_dihedral_angle_4_deg 10.487 r_long_range_B_refined 7.202 r_long_range_B_other 6.904 r_dihedral_angle_1_deg 4.778 r_scangle_other 3.087 r_mcangle_other 2.471 r_mcangle_it 2.464 r_scbond_it 2.018
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.869 r_dihedral_angle_3_deg 10.953 r_dihedral_angle_4_deg 10.487 r_long_range_B_refined 7.202 r_long_range_B_other 6.904 r_dihedral_angle_1_deg 4.778 r_scangle_other 3.087 r_mcangle_other 2.471 r_mcangle_it 2.464 r_scbond_it 2.018 r_scbond_other 2.018 r_mcbond_it 1.537 r_mcbond_other 1.504 r_angle_refined_deg 1.408 r_angle_other_deg 0.672 r_chiral_restr 0.089 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2408 Nucleic Acid Atoms Solvent Atoms 381 Heterogen Atoms 14
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling