9FII | pdb_00009fii

Crystal Structure of oxidized NuoEF variant E222K(NuoF) from Aquifex aeolicus

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 were placed two times independepently in the asymmetric unit

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.1	281	0.1 M Tris pH 7.1, 0.85 M Na3-citrate, 0.1 M NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.072	α = 90
b = 113.397	β = 90
c = 189.555	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	PIXEL	DECTRIS PILATUS 6M		2020-09-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9724	ESRF	ID23-1

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	2.5	48.1	97.3	0.099	0.988	5.6	3.7		47026

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	2.5	2.59			0.467	0.769

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	2.5	47.434	46977	2291	96.516	0.21	0.2076	0.21	0.2494	0.25	Random selection	31.479

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]
0.979			0.025		-1.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.441
r_dihedral_angle_6_deg	13.127
r_dihedral_angle_other_3_deg	13.025
r_dihedral_angle_2_deg	8.791
r_dihedral_angle_1_deg	6.118
r_lrange_it	3.995
r_lrange_other	3.968
r_scangle_it	1.595
r_scangle_other	1.595
r_angle_refined_deg	1.455
r_mcangle_it	1.392
r_mcangle_other	1.392
r_scbond_it	0.921
r_scbond_other	0.921
r_mcbond_it	0.785
r_mcbond_other	0.783
r_angle_other_deg	0.496
r_nbd_other	0.236
r_nbd_refined	0.199
r_symmetry_nbd_other	0.197
r_symmetry_nbd_refined	0.192
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.157
r_symmetry_xyhbond_nbd_refined	0.109
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.068
r_metal_ion_refined	0.063
r_symmetry_xyhbond_nbd_other	0.032
r_chiral_restr_other	0.021
r_bond_refined_d	0.006
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	9072
Nucleic Acid Atoms
Solvent Atoms	351
Heterogen Atoms	126

Software

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