8QH4 | pdb_00008qh4

Crystal structure of reduced 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experimental model	Other		Previously obtained, unpublished and isomorphous structure of oxidized NuoEF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
2.62	53.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.527	α = 90
b = 116.619	β = 90
c = 190.01	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		2018-08-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.0000	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	1.96	48.153	100	0.043	0.999	14.4	13.2		102156			18.86

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	1.96	1.99	100		0.318	0.864	2.6	13.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R-VALUE	1.96	48.153	101256	5246	99.166	0.194	0.1919	0.2	0.2244	0.23	25.256

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]
-0.583			1.355		-0.772

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.795
r_dihedral_angle_3_deg	13.62
r_dihedral_angle_other_3_deg	11.35
r_dihedral_angle_2_deg	7.223
r_dihedral_angle_1_deg	6.208
r_lrange_it	5.711
r_lrange_other	5.547
r_scangle_it	1.573
r_scangle_other	1.477
r_angle_refined_deg	1.152
r_mcangle_it	1.108
r_mcangle_other	1.108
r_scbond_it	0.972
r_scbond_other	0.891
r_mcbond_it	0.666
r_mcbond_other	0.665
r_angle_other_deg	0.4
r_symmetry_xyhbond_nbd_other	0.244
r_symmetry_xyhbond_nbd_refined	0.235
r_nbd_refined	0.215
r_symmetry_nbd_refined	0.192
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.158
r_metal_ion_refined	0.154
r_nbd_other	0.146
r_xyhbond_nbd_other	0.137
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.059
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9084
Nucleic Acid Atoms
Solvent Atoms	872
Heterogen Atoms	214

Software

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