9FIF

Crystal Structure of NuoEF variant P228R(NuoF) from Aquifex aeolicus bound to NADH under anoxic conditions


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6HL2Chains A and B were placed independently two times in the asymmetric unit

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.32810.1 M BisTris pH 6.3, 1.6 M ammonium sulfate, 150 mM NaCl
Crystal Properties
Matthews coefficientSolvent content
2.6954.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.399α = 90
b = 116.035β = 90
c = 189.72γ = 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
11.7748.0371000.0470.9979.26.2136928
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)
11.771.80.4870.721

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-VALUE1.7748.037136826688699.9350.1650.16330.1886Random selection27.176
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]
0.7450.533-1.278
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.61
r_dihedral_angle_other_3_deg13.803
r_dihedral_angle_3_deg11.475
r_dihedral_angle_2_deg6.719
r_dihedral_angle_1_deg6.051
r_lrange_it5.335
r_lrange_other5.105
r_scangle_it2.822
r_scangle_other2.771
r_scbond_it1.746
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.61
r_dihedral_angle_other_3_deg13.803
r_dihedral_angle_3_deg11.475
r_dihedral_angle_2_deg6.719
r_dihedral_angle_1_deg6.051
r_lrange_it5.335
r_lrange_other5.105
r_scangle_it2.822
r_scangle_other2.771
r_scbond_it1.746
r_scbond_other1.712
r_mcangle_it1.565
r_mcangle_other1.565
r_angle_refined_deg1.382
r_mcbond_it1.009
r_mcbond_other1.009
r_angle_other_deg0.486
r_symmetry_nbd_refined0.277
r_nbd_refined0.213
r_nbd_other0.201
r_symmetry_nbd_other0.186
r_nbtor_refined0.184
r_symmetry_xyhbond_nbd_refined0.168
r_xyhbond_nbd_refined0.152
r_symmetry_xyhbond_nbd_other0.135
r_xyhbond_nbd_other0.126
r_symmetry_nbtor_other0.074
r_chiral_restr0.071
r_metal_ion_refined0.049
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9125
Nucleic Acid Atoms
Solvent Atoms992
Heterogen Atoms172

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing