8QHK | pdb_00008qhk

Crystal structure of reduced respiratory Complex I subunits NuoEF from Aquifex aeolicus bound to reduced 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experimental model	Other		Previously solved, isomorphous structure of the same protein, unpublished

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.413	α = 90
b = 116.013	β = 90
c = 189.741	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	1.95	49.538	99.9	0.035	0.999	15.7	13.3		102689			29.08

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	1.95	1.98			0.436	0.737	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R-VALUE	1.95	49.538	102612	5309	99.787	0.168	0.1666	0.18	0.2003	0.21	33.148

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]
-0.298			1.723		-1.425

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.436
r_dihedral_angle_3_deg	13.388
r_dihedral_angle_other_3_deg	12.23
r_dihedral_angle_2_deg	6.687
r_dihedral_angle_1_deg	6.267
r_lrange_it	5.95
r_lrange_other	5.817
r_scangle_it	1.747
r_scangle_other	1.642
r_mcangle_it	1.218
r_mcangle_other	1.217
r_angle_refined_deg	1.137
r_scbond_it	1.104
r_scbond_other	1.025
r_mcbond_it	0.752
r_mcbond_other	0.751
r_angle_other_deg	0.401
r_symmetry_nbd_refined	0.3
r_nbd_other	0.208
r_nbd_refined	0.204
r_symmetry_nbd_other	0.181
r_nbtor_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.17
r_xyhbond_nbd_refined	0.157
r_metal_ion_refined	0.1
r_symmetry_xyhbond_nbd_other	0.094
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	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9069
Nucleic Acid Atoms
Solvent Atoms	932
Heterogen Atoms	231

Software

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