9FIJ | pdb_00009fij

Crystal Structure of reduced NuoEF variant E222K(NuoF) from Aquifex aeolicus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9FII	Rfree flags were transferred from scaled data of isomorphous crystal structure 9FII followed by direct Fourier synthesis using 9FII as starting model

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
2.56	51.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.984	α = 90
b = 113.438	β = 90
c = 189.11	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	2.35	48.687	99.9	0.077	0.996	7.4	6.4		58277

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	2.35	2.41			0.436	0.857

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	2.35	48.687	58200	2853	99.916	0.195	0.1931	0.2	0.2363	0.24	Rfree flags were transferred from scaled data of isomorphous structure (pdb ID 9FII)	36.69

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]
0.901			1.474		-2.375

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.146
r_dihedral_angle_other_3_deg	12.631
r_dihedral_angle_6_deg	12.598
r_dihedral_angle_1_deg	5.861
r_dihedral_angle_2_deg	5.787
r_lrange_it	4.485
r_lrange_other	4.448
r_scangle_it	2.399
r_scangle_other	2.382
r_mcangle_other	1.753
r_mcangle_it	1.752
r_scbond_it	1.444
r_scbond_other	1.415
r_angle_refined_deg	1.296
r_mcbond_it	1.055
r_mcbond_other	1.054
r_angle_other_deg	0.462
r_symmetry_nbd_refined	0.274
r_nbd_other	0.226
r_nbd_refined	0.204
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.141
r_metal_ion_refined	0.135
r_symmetry_xyhbond_nbd_refined	0.086
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.066
r_symmetry_xyhbond_nbd_other	0.054
r_bond_refined_d	0.005
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	9040
Nucleic Acid Atoms
Solvent Atoms	403
Heterogen Atoms	130

Software

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