3HYV

3-D X-Ray structure of the sulfide:quinone oxidoreductase from the hyperthermophilic bacterium Aquifex aeolicus

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	4% PEG 400 (V/V), 0.1M NA-MES (SODIUM 2-(N-MORPHOLINO)-ETHANESULFONATE), 2M AMMONIUM SULFATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.85	α = 90
b = 154.92	β = 90
c = 178.04	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	dynamically bendable mirror	2008-02-24	M	SINGLE WAVELENGTH
2	1	x-ray	100	PIXEL	PSI PILATUS 6M	dynamically bendable mirror	2008-02-24	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.91984	SLS	X10SA
2	SYNCHROTRON	SLS BEAMLINE X06SA	1.14000, 1.14050, 1.13010, 1.03864	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.3	50	97.9	14.87	3.47		135807

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.3	2.4	87.9		3.44	2.47

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MIRAS	THROUGHOUT	2.3	20.04	128783	6821	97.94	0.19534	0.19321	0.23537	RANDOM	38.517

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]
1.32			-0.09		-1.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.217
r_dihedral_angle_4_deg	20.052
r_dihedral_angle_3_deg	15.77
r_dihedral_angle_1_deg	5.351
r_scangle_it	1.654
r_angle_refined_deg	1.254
r_scbond_it	1.043
r_mcangle_it	0.648
r_mcbond_it	0.412
r_nbtor_refined	0.303
r_nbd_refined	0.186
r_symmetry_vdw_refined	0.132
r_xyhbond_nbd_refined	0.119
r_symmetry_hbond_refined	0.088
r_chiral_restr	0.08
r_bond_refined_d	0.01
r_gen_planes_refined	0.003
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 Atoms	Number
Protein Atoms	20016
Nucleic Acid Atoms
Solvent Atoms	571
Heterogen Atoms	768

Software

Software
Software Name	Purpose
XDS	data scaling
SHARP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling