8QGW

Crystal structure of oxidized respiratory Complex I subunits NuoEF from Aquifex aeolicus bound to oxidized 3-acetylpyridine adenine dinucleotide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Previously obtained, unpublished and isomorphous structure of oxidized NuoEF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		281	trisodium citrate, ammonium sulfate, sodium chloride, Tris, BisTris

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.537	α = 90
b = 116.328	β = 90
c = 189.621	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	PIXEL	DECTRIS PILATUS 2M-F		2018-07-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.9116	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.6	49.627	100	0.033	0.999	14.3	13.4		185561			15.97

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.63	100		0.429	0.729	1.8	13.9

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R-VALUE	1.6	49.627	185449	9369	99.959	0.163	0.1618	0.1872	21.269

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]
0.013			0.552		-0.565

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.345
r_dihedral_angle_3_deg	12.766
r_dihedral_angle_other_3_deg	12.542
r_dihedral_angle_2_deg	7.633
r_dihedral_angle_1_deg	6.149
r_lrange_it	5.746
r_lrange_other	5.523
r_scangle_it	2.517
r_scangle_other	2.456
r_scbond_it	1.63
r_scbond_other	1.586
r_angle_refined_deg	1.407
r_mcangle_it	1.367
r_mcangle_other	1.367
r_mcbond_it	0.889
r_mcbond_other	0.889
r_angle_other_deg	0.492
r_symmetry_nbd_refined	0.256
r_nbd_refined	0.224
r_symmetry_xyhbond_nbd_other	0.212
r_nbd_other	0.197
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.154
r_metal_ion_refined	0.124
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.073
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9073
Nucleic Acid Atoms
Solvent Atoms	1209
Heterogen Atoms	220

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
Aimless	data scaling
REFMAC	phasing