9FDV | pdb_00009fdv

Crystal Structure of reduced 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 were transferred from a previously solved isomorphous structure (PDB ID 9FDJ)

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.303	α = 90
b = 116.215	β = 90
c = 189.543	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	1.986	49.587	99.4	0.066	0.994	8	4.6		96723

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	1.986	2.02			0.381	0.807

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	1.986	49.587	96632	4847	99.284	0.167	0.1648	0.18	0.2013	0.21	Transfer from scaled data of PDB-ID 9FDJ	27.952

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]
0.14			1.723		-1.863

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.399
r_dihedral_angle_other_3_deg	12.556
r_dihedral_angle_3_deg	11.837
r_dihedral_angle_2_deg	7.067
r_dihedral_angle_1_deg	6.055
r_lrange_it	5.796
r_lrange_other	5.624
r_scangle_it	2.421
r_scangle_other	2.338
r_scbond_it	1.511
r_scbond_other	1.438
r_angle_refined_deg	1.403
r_mcangle_it	1.39
r_mcangle_other	1.39
r_mcbond_it	0.875
r_mcbond_other	0.874
r_angle_other_deg	0.476
r_metal_ion_refined	0.227
r_nbd_refined	0.217
r_symmetry_nbd_other	0.189
r_symmetry_xyhbond_nbd_refined	0.186
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.171
r_nbd_other	0.167
r_symmetry_nbd_refined	0.141
r_xyhbond_nbd_other	0.097
r_symmetry_xyhbond_nbd_other	0.081
r_symmetry_nbtor_other	0.074
r_symmetry_metal_ion_refined	0.071
r_chiral_restr	0.068
r_bond_refined_d	0.005
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	9100
Nucleic Acid Atoms
Solvent Atoms	849
Heterogen Atoms	172

Software

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