6MO6 | pdb_00006mo6

Crystal structure of the selenomethionine-substituted human sulfide:quinone oxidoreductase

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	500 uL reservoir of 20% (w/v) glycerol, 0.1 M sodium acetate trihydrate pH 4.6, 0.3-0.5 M ammonium acetate, 7-10% (w/v) PEG 4,000, 0.1% (w/v) 1,2-diheptanoyl-sn-glycero-3-phosphocholine (DHPC), 310 uM decylubiquinone (DCQ; stock in 10% (w/v) DHPC) and 10 mM sodium thiosulfate pentahydrate. To the coverslip; apply 1 uL aliquot of 10.66% (w/v) 1-Oleoyl-rac-glycerol (monoolein; stock in ethanol) and air dry for 3 minutes. Add 1uL enzyme followed by 1uL reservoir condition (no mixing).

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.39	α = 90
b = 119.39	β = 90
c = 551.858	γ = 120

Symmetry
Space Group	P 61 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	PIXEL	DECTRIS PILATUS 6M-F		2017-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97918	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.59	68.72	93.7	0.251	0.253	0.027	0.998	22.9	85.7		68911			40.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.59	2.65	60.5		1.655	1.666	0.18	0.646		81.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.59	62.692	1.35	68902	3406	93.32	0.1897	0.1869	0.1867	0.2449	0.2442	39.568

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13040
Nucleic Acid Atoms
Solvent Atoms	277
Heterogen Atoms	216

Software

Software
Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
SHELXCD	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.