9FIF | pdb_00009fif

Crystal Structure of NuoEF variant P228R(NuoF) from Aquifex aeolicus bound to NADH under anoxic conditions

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 independently two times in the asymmetric unit

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.3	281	0.1 M BisTris pH 6.3, 1.6 M ammonium sulfate, 150 mM NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.399	α = 90
b = 116.035	β = 90
c = 189.72	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	1.77	48.037	100	0.047	0.997	9.2	6.2		136928

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	1.77	1.8			0.487	0.721

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	1.77	48.037	136826	6886	99.935	0.165	0.1633	0.17	0.1886	0.2	Random selection	27.176

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]
0.745			0.533		-1.278

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.61
r_dihedral_angle_other_3_deg	13.803
r_dihedral_angle_3_deg	11.475
r_dihedral_angle_2_deg	6.719
r_dihedral_angle_1_deg	6.051
r_lrange_it	5.335
r_lrange_other	5.105
r_scangle_it	2.822
r_scangle_other	2.771
r_scbond_it	1.746
r_scbond_other	1.712
r_mcangle_it	1.565
r_mcangle_other	1.565
r_angle_refined_deg	1.382
r_mcbond_it	1.009
r_mcbond_other	1.009
r_angle_other_deg	0.486
r_symmetry_nbd_refined	0.277
r_nbd_refined	0.213
r_nbd_other	0.201
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.184
r_symmetry_xyhbond_nbd_refined	0.168
r_xyhbond_nbd_refined	0.152
r_symmetry_xyhbond_nbd_other	0.135
r_xyhbond_nbd_other	0.126
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.071
r_metal_ion_refined	0.049
r_bond_refined_d	0.005
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	9125
Nucleic Acid Atoms
Solvent Atoms	992
Heterogen Atoms	172

Software

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