9FDJ

Crystal structure of the NuoEF variant R66G (NuoF) from Aquifex aeolicus bound to NADH under anoxic conditions (short soak)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6HL2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.3281100 mM BisTris pH 6.3, 1.4 M ammonium sulfate, 100 mM NaCl
Crystal Properties
Matthews coefficientSolvent content
2.5952.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.241α = 90
b = 116.156β = 90
c = 189.026γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-09-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.9724ESRFID23-1

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
11.747.93299.90.0340.99911.65.8153510
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)
11.71.730.4270.7871.6

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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.747.932153402778899.9010.1590.15810.184Random selection28.128
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]
0.8830.813-1.696
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.206
r_dihedral_angle_other_3_deg13.307
r_dihedral_angle_3_deg11.607
r_dihedral_angle_2_deg6.652
r_dihedral_angle_1_deg6.012
r_lrange_it5.588
r_lrange_other5.421
r_scangle_it3.322
r_scangle_other3.249
r_scbond_it2.108
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.206
r_dihedral_angle_other_3_deg13.307
r_dihedral_angle_3_deg11.607
r_dihedral_angle_2_deg6.652
r_dihedral_angle_1_deg6.012
r_lrange_it5.588
r_lrange_other5.421
r_scangle_it3.322
r_scangle_other3.249
r_scbond_it2.108
r_scbond_other2.051
r_mcangle_it1.714
r_mcangle_other1.713
r_angle_refined_deg1.482
r_mcbond_it1.151
r_mcbond_other1.146
r_angle_other_deg0.515
r_nbd_refined0.22
r_symmetry_nbd_other0.187
r_symmetry_xyhbond_nbd_refined0.187
r_nbtor_refined0.184
r_nbd_other0.166
r_metal_ion_refined0.165
r_xyhbond_nbd_refined0.141
r_xyhbond_nbd_other0.118
r_symmetry_nbd_refined0.089
r_chiral_restr0.077
r_symmetry_nbtor_other0.075
r_chiral_restr_other0.026
r_symmetry_xyhbond_nbd_other0.025
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9081
Nucleic Acid Atoms
Solvent Atoms882
Heterogen Atoms205

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing