3HYW

3-D X-Ray structure of the sulfide:quinone oxidoreductase of the hyperthermophilic bacterium Aquifex aeolicus in complex with decylubiquinone


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62914% PEG 400, 2M AMMONIUM SULFATE, 0.1M NA-ACETATE, PH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.6253.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.78α = 90
b = 154.01β = 90
c = 175.55γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDDYNAMICALLY BENDABLE MIRROR2008-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.00150SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
125096.213.174.74194489
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.176.71.861.86

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3H27220.45184559975796.220.201520.199720.2357RANDOM35.976
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]
0.87-0.74-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.295
r_dihedral_angle_4_deg18.421
r_dihedral_angle_3_deg14.453
r_dihedral_angle_1_deg5.361
r_scangle_it1.628
r_angle_refined_deg1.151
r_scbond_it1.04
r_mcangle_it0.654
r_mcbond_it0.424
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.295
r_dihedral_angle_4_deg18.421
r_dihedral_angle_3_deg14.453
r_dihedral_angle_1_deg5.361
r_scangle_it1.628
r_angle_refined_deg1.151
r_scbond_it1.04
r_mcangle_it0.654
r_mcbond_it0.424
r_nbtor_refined0.307
r_nbd_refined0.188
r_symmetry_vdw_refined0.185
r_symmetry_hbond_refined0.172
r_xyhbond_nbd_refined0.117
r_chiral_restr0.071
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms20036
Nucleic Acid Atoms
Solvent Atoms1137
Heterogen Atoms829

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing