9HEG | pdb_00009heg

Crystal structure of the oxidized respiratory complex I subunit NuoEF from Aquifex aeolicus, mutation V136M(NuoE)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		An unpublished structure of NuoEF_V90P_V136M was used as search model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		281	0.1 M BisTris, 1.35-1.45 M ammonium sulfate, 100 mM NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.22	α = 90
b = 67.413	β = 104.839
c = 121.931	γ = 90

Symmetry
Space Group	P 1 21 1

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 6M		2018-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0000	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	2.05	45.62	97.8	0.059	0.997	10.2	7.1		85028

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	2.05	2.09			0.403	0.798	2.2

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.05	45.62	85010	4359	97.583	0.224	0.2226	0.2292	0.2581	0.2663	Random selection	26.665

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]
0.311		-0.629	0.346		-0.284

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.657
r_dihedral_angle_3_deg	13.338
r_dihedral_angle_other_3_deg	12.132
r_dihedral_angle_2_deg	6.197
r_dihedral_angle_1_deg	5.895
r_lrange_it	2.716
r_lrange_other	2.578
r_angle_refined_deg	1.08
r_scangle_it	0.796
r_scangle_other	0.785
r_mcangle_it	0.653
r_mcangle_other	0.653
r_scbond_it	0.609
r_scbond_other	0.604
r_angle_other_deg	0.382
r_mcbond_it	0.375
r_mcbond_other	0.375
r_nbd_refined	0.201
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.179
r_nbd_other	0.157
r_symmetry_nbd_refined	0.149
r_xyhbond_nbd_refined	0.135
r_symmetry_xyhbond_nbd_refined	0.095
r_symmetry_nbtor_other	0.073
r_metal_ion_refined	0.063
r_chiral_restr	0.055
r_chiral_restr_other	0.011
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9088
Nucleic Acid Atoms
Solvent Atoms	694
Heterogen Atoms	128

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing