8QH7

Crystal structure of respiratory Complex I subunits NuoEF from Aquifex aeolicus bound to reduced 3-acetylpyridine adenine dinucleotide (without reducing agent)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherUnpublished, isomorphous structure of oxidized NuoEF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP281trisodium citrate, ammonium sulfate, sodium chloride, Tris, BisTris
Crystal Properties
Matthews coefficientSolvent content
2.6152.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.233α = 90
b = 116.449β = 90
c = 190.047γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-06-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.9999SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.8549.799.90.0390.99913.613.512043818.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.8899.90.4210.8482.113.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISFREE R-VALUE1.8549.695120344620199.9190.1720.17080.200627.406
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]
1.0630.2-1.263
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.804
r_dihedral_angle_3_deg13.407
r_dihedral_angle_other_3_deg12.675
r_dihedral_angle_2_deg6.766
r_lrange_it6.231
r_dihedral_angle_1_deg6.175
r_lrange_other5.967
r_scangle_it1.781
r_scangle_other1.781
r_angle_refined_deg1.165
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.804
r_dihedral_angle_3_deg13.407
r_dihedral_angle_other_3_deg12.675
r_dihedral_angle_2_deg6.766
r_lrange_it6.231
r_dihedral_angle_1_deg6.175
r_lrange_other5.967
r_scangle_it1.781
r_scangle_other1.781
r_angle_refined_deg1.165
r_scbond_it1.132
r_scbond_other1.132
r_mcangle_other1.116
r_mcangle_it1.115
r_mcbond_it0.704
r_mcbond_other0.702
r_angle_other_deg0.404
r_symmetry_xyhbond_nbd_refined0.302
r_symmetry_nbd_refined0.247
r_nbd_refined0.209
r_nbd_other0.209
r_symmetry_nbd_other0.181
r_nbtor_refined0.18
r_symmetry_metal_ion_refined0.15
r_xyhbond_nbd_refined0.144
r_metal_ion_refined0.123
r_symmetry_nbtor_other0.073
r_symmetry_xyhbond_nbd_other0.073
r_chiral_restr0.059
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9083
Nucleic Acid Atoms
Solvent Atoms1065
Heterogen Atoms250

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
Aimlessdata scaling
REFMACphasing