9FIL | pdb_00009fil

Crystal Structure of reduced NuoEF variant E222K(NuoF) from Aquifex aeolicus bound to NAD+

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6HLI	Ensemble comprising chains A and B was placed twice 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
2.71	54.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.136	α = 90
b = 115.539	β = 90
c = 189.92	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	2.54	49.403	99.3	0.139	0.976	5.2	3.9		47056

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	2.54	2.63			0.462	0.757

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	2.54	49.403	47000	2370	99.041	0.203	0.2006	0.21	0.2478	0.25	Random selection	20.459

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]
1.117			0.559		-1.676

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_3_deg	18.321
r_dihedral_angle_3_deg	13.452
r_dihedral_angle_6_deg	12.64
r_dihedral_angle_2_deg	10.387
r_dihedral_angle_1_deg	5.82
r_lrange_it	3.301
r_lrange_other	3.252
r_angle_refined_deg	1.461
r_mcangle_it	1.208
r_mcangle_other	1.208
r_scangle_it	1.146
r_scangle_other	1.146
r_mcbond_it	0.666
r_mcbond_other	0.666
r_scbond_it	0.648
r_scbond_other	0.648
r_angle_other_deg	0.512
r_nbd_refined	0.209
r_symmetry_nbd_other	0.198
r_nbtor_refined	0.181
r_nbd_other	0.154
r_xyhbond_nbd_refined	0.147
r_symmetry_xyhbond_nbd_refined	0.119
r_metal_ion_refined	0.107
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.072
r_symmetry_xyhbond_nbd_other	0.048
r_symmetry_nbd_refined	0.047
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	9048
Nucleic Acid Atoms
Solvent Atoms	418
Heterogen Atoms	186

Software

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