6R7P

Crystal structure of oxidized Aquifex aeolicus NADH-quinone oxidoreductase subunits NuoE and NuoF S96M

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6Q9K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	6.5	289	(NH4)2SO4, BisTris, NaCl, cryo-protection with glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.41	α = 90
b = 114.64	β = 90
c = 187.87	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	CCD	RIGAKU SATURN 944+		2019-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54187

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	3.22	38.21	99.8	0.269	0.291	0.11	0.991	6.8	6.7		22909

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.22	3.48	100		0.89	0.964	0.367	0.795		6.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6Q9K	3.22	31.73	21749	1112	99.63	0.2104	0.2079	0.2572	RANDOM	60.227

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]
-1.66			2.43		-0.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.807
r_dihedral_angle_3_deg	16.177
r_dihedral_angle_4_deg	12.914
r_dihedral_angle_1_deg	6.673
r_angle_refined_deg	1.321
r_angle_other_deg	1.121
r_chiral_restr	0.053
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.807
r_dihedral_angle_3_deg	16.177
r_dihedral_angle_4_deg	12.914
r_dihedral_angle_1_deg	6.673
r_angle_refined_deg	1.321
r_angle_other_deg	1.121
r_chiral_restr	0.053
r_bond_refined_d	0.005
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	9104
Nucleic Acid Atoms
Solvent Atoms	111
Heterogen Atoms	101

Software

Software
Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.