9FIH | pdb_00009fih

Crystal Structure of NuoEF variant P228R(NuoF) from Aquifex aeolicus bound to NADH under anoxic conditions after 10 min soaking

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9FIF	Rfree flags were transferred from scaled data of an isomorphous crystal of the same variant followed by direct Fourier synthesis using 9FIF as initial model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.9	281	0.1 M BisTris pH 6.9, 1.55 M ammonium sulfate, 150 mM NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.522	α = 90
b = 116.359	β = 90
c = 190.184	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	2.08	48.143	99.8	0.097	0.992	6.3	4.3		85376

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	2.08	2.12			0.498	0.687

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	FOURIER SYNTHESIS	FREE R-VALUE	2.08	48.143	85297	4272	99.67	0.18	0.1786	0.19	0.213	0.22	Rfree flags were transferred from scaled data of an isomorphous crystal of the same variant	24.32

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]
0.286			0.377		-0.663

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_3_deg	13.621
r_dihedral_angle_6_deg	13.325
r_dihedral_angle_3_deg	11.91
r_dihedral_angle_2_deg	7.492
r_dihedral_angle_1_deg	6.119
r_lrange_it	3.803
r_lrange_other	3.574
r_scangle_it	1.607
r_scangle_other	1.511
r_angle_refined_deg	1.41
r_scbond_it	0.971
r_mcangle_other	0.965
r_mcangle_it	0.964
r_scbond_other	0.908
r_mcbond_it	0.566
r_mcbond_other	0.562
r_angle_other_deg	0.488
r_nbd_refined	0.212
r_symmetry_xyhbond_nbd_refined	0.199
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.167
r_nbd_other	0.158
r_symmetry_nbd_refined	0.118
r_xyhbond_nbd_other	0.111
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.068
r_symmetry_xyhbond_nbd_other	0.056
r_metal_ion_refined	0.02
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	9110
Nucleic Acid Atoms
Solvent Atoms	924
Heterogen Atoms	228

Software

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