9HE5 | pdb_00009he5

Crystal structure of the oxidized respiratory complex I subunit NuoEF from Aquifex aeolicus, mutation V90P(NuoE)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M Tris pH 6.8-7.1, 0.8-1.05 M Na3Citrat, 0.1 M NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.246	α = 90
b = 64.326	β = 106.347
c = 121.576	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	MIRRORS	2012-10-25	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)	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	1.84	116.661	99.7	0.071	0.083	0.042	0.998	13.7	3.7		122759

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	1.84	2.06		99.9	0.461	0.539	0.275	0.857		3.7

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	1.844	116.661	122736	6164	99.634	0.169	0.1678	0.1794	0.1899	0.1998	Random selection	27.11

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]
-0.714		-1.322	0.391		0.938

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.367
r_dihedral_angle_3_deg	12.037
r_dihedral_angle_1_deg	5.92
r_dihedral_angle_2_deg	5.918
r_lrange_it	4.84
r_lrange_other	4.771
r_scangle_other	3.57
r_scangle_it	3.569
r_mcangle_it	2.285
r_mcangle_other	2.285
r_scbond_other	2.163
r_scbond_it	2.162
r_mcbond_it	1.484
r_mcbond_other	1.484
r_angle_refined_deg	1.309
r_angle_other_deg	0.456
r_nbd_refined	0.208
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.143
r_metal_ion_refined	0.143
r_nbd_other	0.131
r_symmetry_xyhbond_nbd_refined	0.104
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.069
r_symmetry_nbd_refined	0.056
r_chiral_restr_other	0.024
r_symmetry_xyhbond_nbd_other	0.022
r_gen_planes_refined	0.005
r_bond_refined_d	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	9082
Nucleic Acid Atoms
Solvent Atoms	592
Heterogen Atoms	98

Software

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