9HEN | pdb_00009hen

Crystal structure of the oxidized respiratory complex I subunit NuoEF from Aquifex aeolicus, double mutation V90P and V136M(NuoE), bound to NAD+

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6HL2	chains A and B of 6HL2 were used as search model, placed two times in the ASU

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, 0.1 M NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.878	α = 90
b = 64.19	β = 107.744
c = 124.115	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		2017-03-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.9999	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	2.27	48.24	99.1	0.044	0.998	12.8	7		66804

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	2.27	2.32			0.286	0.857

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	2.27	48.24	66768	3322	98.869	0.163	0.1621	0.1697	0.1825	0.1867	Random selection	33.796

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]
-1.395		-0.806	0.327		1.314

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_3_deg	19.422
r_dihedral_angle_6_deg	13.525
r_dihedral_angle_3_deg	12.344
r_dihedral_angle_1_deg	5.627
r_dihedral_angle_2_deg	4.818
r_lrange_it	4.373
r_lrange_other	4.246
r_scangle_it	1.737
r_scangle_other	1.737
r_mcangle_it	1.522
r_mcangle_other	1.522
r_angle_refined_deg	1.126
r_scbond_it	1.038
r_scbond_other	1.038
r_mcbond_it	0.856
r_mcbond_other	0.856
r_angle_other_deg	0.397
r_nbd_refined	0.196
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.179
r_nbd_other	0.156
r_xyhbond_nbd_refined	0.142
r_symmetry_nbd_refined	0.142
r_symmetry_xyhbond_nbd_refined	0.102
r_symmetry_nbtor_other	0.072
r_metal_ion_refined	0.068
r_chiral_restr	0.057
r_chiral_restr_other	0.013
r_bond_refined_d	0.004
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	9144
Nucleic Acid Atoms
Solvent Atoms	723
Heterogen Atoms	173

Software

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