9FE7 | pdb_00009fe7

Crystal Structure of oxidized NuoEF variant P228R(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	6HL2	Chains A and B were used as ensemble, which was placed two times to fill the asymmetric unit

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.3	281	100 mM BisTris pH 6.3, 1.65 M ammonium sulfate, 150 mM NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.283	α = 90
b = 116.13	β = 90
c = 189.842	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	2.28	48.001	98	0.089	0.982	5.7	4		63251

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	2.28	2.34			0.323	0.797

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	2.28	48.001	62976	3160	97.293	0.2	0.1975	0.21	0.2443	0.25	Random selection	23.267

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]
-1.186			2.524		-1.337

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_3_deg	15.306
r_dihedral_angle_6_deg	13.485
r_dihedral_angle_3_deg	12.908
r_dihedral_angle_2_deg	8.235
r_dihedral_angle_1_deg	6.429
r_lrange_it	3.094
r_lrange_other	2.905
r_angle_refined_deg	1.463
r_scangle_it	1.32
r_scangle_other	1.269
r_scbond_it	0.844
r_mcangle_it	0.796
r_mcangle_other	0.796
r_scbond_other	0.794
r_angle_other_deg	0.513
r_mcbond_it	0.472
r_mcbond_other	0.472
r_nbd_refined	0.217
r_symmetry_nbd_refined	0.208
r_symmetry_nbd_other	0.191
r_symmetry_xyhbond_nbd_refined	0.19
r_nbtor_refined	0.183
r_nbd_other	0.167
r_xyhbond_nbd_refined	0.163
r_metal_ion_refined	0.136
r_symmetry_xyhbond_nbd_other	0.078
r_chiral_restr	0.075
r_symmetry_nbtor_other	0.074
r_chiral_restr_other	0.018
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	9089
Nucleic Acid Atoms
Solvent Atoms	726
Heterogen Atoms	161

Software

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