3H8I

The first X-ray structure of a sulfide:quinone oxidoreductase: Insights into sulfide oxidation mechanism


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52932.2 M NH4H2PO4, 100 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2VAPOR DIFFUSION, HANGING DROP4.52932.2 M NH4H2PO4/K2HPO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 178.55α = 90
b = 178.55β = 90
c = 162.31γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102004-04-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.934ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.6547.430.08210.23.544293271.62
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.652.899.90.50423.66392

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSIRASTHROUGHOUT2.6526.6644225223598.960.1970.19550.2246RANDOM56.84
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]
-0.4377-0.43770.8754
RMS Deviations
KeyRefinement Restraint Deviation
t_dihedral_angle_d16.24
t_it0.914
t_angle_deg0.907
t_gen_planes0.012
t_bond_d0.006
t_trig_c_planes0.006
t_nbd
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5588
Nucleic Acid Atoms
Solvent Atoms171
Heterogen Atoms157

Software

Software
Software NamePurpose
DNAdata collection
SHARPphasing
BUSTER-TNTrefinement
XDSdata reduction
SCALAdata scaling