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Crystal structure of sulfide:quinone oxidoreductase Cys128Ser variant from Acidithiobacillus ferrooxidans in complex with decylubiquinone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3T31 PDB ENTRY 3T31
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 295 30% PEG 600, 0.1 M bis-tris buffer,0.1 M MgSO4, 0.05% DDM, 5 mM decylubiquinone, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.76 55.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.907 α = 90 b = 149.907 β = 90 c = 81.386 γ = 120
Symmetry Space Group P 62 2 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 2010-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97945 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 75 100 0.16 19 21.5 27876 27876
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 2.2 2.32 100 1.113 1.113 3.1 21.6
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION refinement PDB ENTRY 3T31 2.2 50.748 1.35 27876 1344 99.99 0.1704 0.1678 0.1633 0.219 0.2138
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] -4.5451 -4.5451 9.0903
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.401 f_angle_d 1.109 f_chiral_restr 0.069 f_plane_restr 0.008 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3222 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 120
Software Software Software Name Purpose XDS data scaling PHENIX model building PHENIX refinement MOSFLM data reduction SCALA data scaling PHENIX phasing