9FE5 | pdb_00009fe5

Crystal Structure of NuoEF variant R66G(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	9FDJ	RFree flags were transferred from the scaled data of the previously solved structure 9FDJ, followed by direct Fourier synthesis

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	281	100 mM BisTris pH 6.5, 1.4 M ammonium sulfate, 100 mM NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.184	α = 90
b = 116.158	β = 90
c = 189.651	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	2.1	47.948	99.8	0.064	0.996	8.5	6		82223

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	2.1	2.14			0.476	0.776	1.9

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	2.1	47.948	80830	4065	98.158	0.182	0.1803	0.19	0.22	0.23	Rfree flags were transferred from scaled data of previously solved structure 9FDJ	32.922

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]
-0.921			1.74		-0.818

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.579
r_dihedral_angle_other_3_deg	13.547
r_dihedral_angle_3_deg	11.651
r_dihedral_angle_1_deg	6.186
r_dihedral_angle_2_deg	5.759
r_lrange_it	5.209
r_lrange_other	5.118
r_scangle_it	1.754
r_scangle_other	1.668
r_mcangle_it	1.219
r_mcangle_other	1.219
r_angle_refined_deg	1.2
r_scbond_it	1.051
r_scbond_other	0.994
r_mcbond_it	0.727
r_mcbond_other	0.727
r_angle_other_deg	0.423
r_nbd_refined	0.21
r_symmetry_xyhbond_nbd_refined	0.187
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.182
r_xyhbond_nbd_other	0.177
r_metal_ion_refined	0.17
r_nbd_other	0.153
r_xyhbond_nbd_refined	0.142
r_symmetry_nbd_refined	0.136
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.061
r_symmetry_xyhbond_nbd_other	0.021
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	9105
Nucleic Acid Atoms
Solvent Atoms	778
Heterogen Atoms	236

Software

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