9HEM | pdb_00009hem

Crystal structure of the oxidized respiratory complex I subunit NuoEF from Aquifex aeolicus, mutation 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	Other		An in-house model of the same protein without nucleotide (now pdb ID 9HEG) was used

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
2.58	52.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.723	α = 90
b = 63.372	β = 107.258
c = 123.429	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		2018-06-11	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	2.6	46.2	99.5	0.067	0.996	9.2	7.1		42296

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	2.6	2.7	99.7		0.447	0.8	1.8	7.2

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	2.6	46.2	42278	2154	99.347	0.248	0.2456	0.2518	0.2901	0.2954	Random selection	43.067

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]
0.884		-3.318	1.548		-0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.99
r_dihedral_angle_6_deg	13.094
r_dihedral_angle_other_3_deg	12.236
r_dihedral_angle_2_deg	5.76
r_dihedral_angle_1_deg	5.536
r_lrange_it	3.806
r_lrange_other	3.796
r_scangle_it	1.444
r_scangle_other	1.406
r_mcangle_it	1.322
r_mcangle_other	1.322
r_angle_refined_deg	1.186
r_scbond_it	0.901
r_scbond_other	0.845
r_mcbond_it	0.779
r_mcbond_other	0.779
r_angle_other_deg	0.416
r_symmetry_xyhbond_nbd_refined	0.239
r_nbd_refined	0.2
r_symmetry_nbd_other	0.2
r_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.18
r_nbd_other	0.166
r_symmetry_nbd_refined	0.153
r_symmetry_xyhbond_nbd_other	0.145
r_metal_ion_refined	0.108
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.056
r_chiral_restr_other	0.015
r_bond_refined_d	0.004
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	9065
Nucleic Acid Atoms
Solvent Atoms	153
Heterogen Atoms	196

Software

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