8QH7

Crystal structure of respiratory Complex I subunits NuoEF from Aquifex aeolicus bound to reduced 3-acetylpyridine adenine dinucleotide (without reducing agent)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Unpublished, isomorphous structure of oxidized NuoEF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	52.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.233	α = 90
b = 116.449	β = 90
c = 190.047	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 EIGER X 16M		2018-06-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.9999	SLS	X06SA

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	1.85	49.7	99.9	0.039	0.999	13.6	13.5		120438			18.8

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	1.85	1.88	99.9		0.421	0.848	2.1	13.3

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	1.85	49.695	120344	6201	99.919	0.172	0.1708	0.2006	27.406

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]
1.063			0.2		-1.263

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.804
r_dihedral_angle_3_deg	13.407
r_dihedral_angle_other_3_deg	12.675
r_dihedral_angle_2_deg	6.766
r_lrange_it	6.231
r_dihedral_angle_1_deg	6.175
r_lrange_other	5.967
r_scangle_it	1.781
r_scangle_other	1.781
r_angle_refined_deg	1.165
r_scbond_it	1.132
r_scbond_other	1.132
r_mcangle_other	1.116
r_mcangle_it	1.115
r_mcbond_it	0.704
r_mcbond_other	0.702
r_angle_other_deg	0.404
r_symmetry_xyhbond_nbd_refined	0.302
r_symmetry_nbd_refined	0.247
r_nbd_refined	0.209
r_nbd_other	0.209
r_symmetry_nbd_other	0.181
r_nbtor_refined	0.18
r_symmetry_metal_ion_refined	0.15
r_xyhbond_nbd_refined	0.144
r_metal_ion_refined	0.123
r_symmetry_nbtor_other	0.073
r_symmetry_xyhbond_nbd_other	0.073
r_chiral_restr	0.059
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9083
Nucleic Acid Atoms
Solvent Atoms	1065
Heterogen Atoms	250

Software

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