8QG1

Crystal structure of oxidized respiratory Complex I subunits NuoEF from Aquifex aeolicus bound to ADP-ribose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		isomorphous structure from unpublished inhouse data

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
2.59	52.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.129	α = 90
b = 116.146	β = 90
c = 189.485	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		2018-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.000	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	2	49.561	99.8	0.039	0.999	12.8	13.6		94748		1.5	31.47

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	2	2.03	99.9		0.567	0.777	1.6	14.2

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	2	49.561	94668	4892	99.685	0.179	0.1775	0.2071	35.457

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]
-0.623			1.771		-1.149

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_3_deg	19.781
r_dihedral_angle_6_deg	14.252
r_dihedral_angle_3_deg	12.662
r_dihedral_angle_1_deg	6.165
r_lrange_it	5.481
r_lrange_other	5.377
r_dihedral_angle_2_deg	5.298
r_scangle_it	1.652
r_scangle_other	1.605
r_mcangle_it	1.201
r_mcangle_other	1.201
r_scbond_it	1.035
r_angle_refined_deg	1.029
r_scbond_other	0.999
r_mcbond_it	0.753
r_mcbond_other	0.752
r_angle_other_deg	0.355
r_nbd_refined	0.2
r_nbd_other	0.188
r_nbtor_refined	0.18
r_symmetry_nbd_other	0.179
r_symmetry_nbd_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.17
r_xyhbond_nbd_refined	0.155
r_metal_ion_refined	0.139
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.053
r_symmetry_xyhbond_nbd_other	0.04
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9092
Nucleic Acid Atoms
Solvent Atoms	868
Heterogen Atoms	216

Software

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