9FDJ

Crystal structure of the NuoEF variant R66G (NuoF) from Aquifex aeolicus bound to NADH under anoxic conditions (short soak)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6HL2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.3	281	100 mM BisTris pH 6.3, 1.4 M ammonium sulfate, 100 mM NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.241	α = 90
b = 116.156	β = 90
c = 189.026	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	1.7	47.932	99.9	0.034	0.999	11.6	5.8		153510

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	1.7	1.73			0.427	0.787	1.6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.7	47.932	153402	7788	99.901	0.159	0.1581	0.184	Random selection	28.128

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]
0.883			0.813		-1.696

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.206
r_dihedral_angle_other_3_deg	13.307
r_dihedral_angle_3_deg	11.607
r_dihedral_angle_2_deg	6.652
r_dihedral_angle_1_deg	6.012
r_lrange_it	5.588
r_lrange_other	5.421
r_scangle_it	3.322
r_scangle_other	3.249
r_scbond_it	2.108
r_scbond_other	2.051
r_mcangle_it	1.714
r_mcangle_other	1.713
r_angle_refined_deg	1.482
r_mcbond_it	1.151
r_mcbond_other	1.146
r_angle_other_deg	0.515
r_nbd_refined	0.22
r_symmetry_nbd_other	0.187
r_symmetry_xyhbond_nbd_refined	0.187
r_nbtor_refined	0.184
r_nbd_other	0.166
r_metal_ion_refined	0.165
r_xyhbond_nbd_refined	0.141
r_xyhbond_nbd_other	0.118
r_symmetry_nbd_refined	0.089
r_chiral_restr	0.077
r_symmetry_nbtor_other	0.075
r_chiral_restr_other	0.026
r_symmetry_xyhbond_nbd_other	0.025
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9081
Nucleic Acid Atoms
Solvent Atoms	882
Heterogen Atoms	205

Software

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