6Q9K | pdb_00006q9k

Crystal structure of reduced Aquifex aeolicus NADH-quinone oxidoreductase subunits NuoE and NuoF S96M bound to NADH

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	6.25	281	(NH4)2SO4, BisTris, NaCl, cryo-protection with glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.38	α = 90
b = 115.94	β = 90
c = 189.97	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+		2018-12-07	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	1.99	21.26	99.8	0.182	0.2	0.081	0.992	6.9	5.8		96646

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	1.99	2.02	99.3		0.867	0.961	0.403	0.699		5

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	1.99	21.26	91590	4988	99.71	0.1895	0.1879	0.2	0.2186	0.23	RANDOM	21.726

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]
0.69			0.29		-0.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.272
r_dihedral_angle_4_deg	13.861
r_dihedral_angle_3_deg	13.248
r_dihedral_angle_1_deg	6.414
r_angle_refined_deg	1.273
r_angle_other_deg	1.194
r_chiral_restr	0.061
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.272
r_dihedral_angle_4_deg	13.861
r_dihedral_angle_3_deg	13.248
r_dihedral_angle_1_deg	6.414
r_angle_refined_deg	1.273
r_angle_other_deg	1.194
r_chiral_restr	0.061
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	9108
Nucleic Acid Atoms
Solvent Atoms	959
Heterogen Atoms	228

Software

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

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.