9FEA | pdb_00009fea

Crystal Structure of reduced NuoEF variant P228R(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	6HL2	Chains A and B were used as ensemble that was placed two times independently in the asymmetric unit

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	281	100 mM BisTris pH 6.5, 1.6 M ammonium sulfate, 150 mM NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.582	α = 90
b = 115.785	β = 90
c = 190.011	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	1.66	49.486	97.2	0.064	0.993	6.9	4		161000

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	1.66	1.69			0.506	0.62

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	1.66	49.486	160798	7928	96.865	0.174	0.1729	0.18	0.1963	0.21	Random selection	22.061

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]
0.196			0.732		-0.928

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.093
r_dihedral_angle_other_3_deg	14.795
r_dihedral_angle_3_deg	11.391
r_dihedral_angle_2_deg	7.829
r_lrange_it	6.046
r_dihedral_angle_1_deg	6.031
r_lrange_other	5.876
r_scangle_it	2.56
r_scangle_other	2.487
r_scbond_it	1.614
r_mcangle_it	1.579
r_mcangle_other	1.579
r_scbond_other	1.565
r_angle_refined_deg	1.476
r_mcbond_it	0.951
r_mcbond_other	0.95
r_angle_other_deg	0.517
r_nbd_refined	0.224
r_xyhbond_nbd_other	0.201
r_nbd_other	0.192
r_symmetry_nbd_other	0.191
r_metal_ion_refined	0.188
r_nbtor_refined	0.185
r_symmetry_nbd_refined	0.175
r_xyhbond_nbd_refined	0.162
r_symmetry_xyhbond_nbd_refined	0.16
r_symmetry_xyhbond_nbd_other	0.103
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.075
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9138
Nucleic Acid Atoms
Solvent Atoms	1156
Heterogen Atoms	211

Software

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