9FEA

Crystal Structure of reduced NuoEF variant P228R(NuoF) from Aquifex aeolicus bound to NAD+


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5281100 mM BisTris pH 6.5, 1.6 M ammonium sulfate, 150 mM NaCl
Crystal Properties
Matthews coefficientSolvent content
2.652.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.582α = 90
b = 115.785β = 90
c = 190.011γ = 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
11.6649.48697.20.0640.9936.94161000
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)
11.661.690.5060.62

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-VALUE1.6649.486160798792896.8650.1740.17290.1963Random selection22.061
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]
0.1960.732-0.928
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.093
r_dihedral_angle_other_3_deg14.795
r_dihedral_angle_3_deg11.391
r_dihedral_angle_2_deg7.829
r_lrange_it6.046
r_dihedral_angle_1_deg6.031
r_lrange_other5.876
r_scangle_it2.56
r_scangle_other2.487
r_scbond_it1.614
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.093
r_dihedral_angle_other_3_deg14.795
r_dihedral_angle_3_deg11.391
r_dihedral_angle_2_deg7.829
r_lrange_it6.046
r_dihedral_angle_1_deg6.031
r_lrange_other5.876
r_scangle_it2.56
r_scangle_other2.487
r_scbond_it1.614
r_mcangle_it1.579
r_mcangle_other1.579
r_scbond_other1.565
r_angle_refined_deg1.476
r_mcbond_it0.951
r_mcbond_other0.95
r_angle_other_deg0.517
r_nbd_refined0.224
r_xyhbond_nbd_other0.201
r_nbd_other0.192
r_symmetry_nbd_other0.191
r_metal_ion_refined0.188
r_nbtor_refined0.185
r_symmetry_nbd_refined0.175
r_xyhbond_nbd_refined0.162
r_symmetry_xyhbond_nbd_refined0.16
r_symmetry_xyhbond_nbd_other0.103
r_symmetry_nbtor_other0.076
r_chiral_restr0.075
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9138
Nucleic Acid Atoms
Solvent Atoms1156
Heterogen Atoms211

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing