3SX6 | pdb_00003sx6

Crystal structure of sulfide:quinone oxidoreductase Cys356Ala variant from Acidithiobacillus ferrooxidans complexed with decylubiquinone

X-RAY DIFFRACTION

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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, 2 mM decylubiquinone, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 149.828	α = 90
b = 149.828	β = 90
c = 81.513	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		2009-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97949	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.7955	50	92.2	0.067	0.067	32.2	11.8	50553	46610

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	1.7955	1.86	64.5		0.749	0.749	1.83	8.6	3202

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	1.7955	30.14	1.34	50587	46540	2376	91.97	0.1809	0.1788	0.1773	0.2198	0.2164	RANDOM

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]
-6.1212			-6.1212		12.2423

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	20.593
f_angle_d	1.078
f_chiral_restr	0.076
f_plane_restr	0.008
f_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3221
Nucleic Acid Atoms
Solvent Atoms	341
Heterogen Atoms	125

Software

Software
Software Name	Purpose
XDS	data scaling
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing