9FDK

Crystal Structure of oxidized NuoEF variant R66G(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	9FDJ	Rfree flags transferred from isomorphous data set of NuoEF_R66G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.3	281	0.1 M BisTris pH 6.3, 1.4 M ammonium sulfate, 100 mM NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.283	α = 90
b = 116.318	β = 90
c = 189.318	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	1.8	63.3	99.9	0.042	0.998	11	6.3		130020

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	1.8	1.83			0.456	0.787	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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R-VALUE	1.8	60.091	129899	6583	99.82	0.157	0.1558	0.1864	Random selection	27.098

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]
0.184			1.248		-1.432

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.678
r_dihedral_angle_other_3_deg	13.015
r_dihedral_angle_3_deg	11.567
r_dihedral_angle_2_deg	6.741
r_dihedral_angle_1_deg	5.985
r_lrange_it	5.17
r_lrange_other	5.055
r_scangle_it	3.221
r_scangle_other	3.136
r_scbond_it	2.018
r_scbond_other	1.951
r_mcangle_it	1.547
r_mcangle_other	1.547
r_angle_refined_deg	1.434
r_mcbond_it	1.048
r_mcbond_other	1.045
r_angle_other_deg	0.498
r_metal_ion_refined	0.275
r_symmetry_xyhbond_nbd_refined	0.221
r_nbd_refined	0.215
r_nbd_other	0.186
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.182
r_symmetry_nbd_refined	0.173
r_xyhbond_nbd_refined	0.147
r_xyhbond_nbd_other	0.121
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.073
r_chiral_restr_other	0.031
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	9103
Nucleic Acid Atoms
Solvent Atoms	886
Heterogen Atoms	173

Software

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