9FE8

Crystal Structure of reduced NuoEF variant P228R(NuoF) from Aquifex aeolicus


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.3281100 mM BisTris pH 6.3, 1.65 M ammonium sulfate, 150 mM NaCl
Crystal Properties
Matthews coefficientSolvent content
2.652.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.084α = 90
b = 116.217β = 90
c = 190.26γ = 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
12.3449.6381000.0680.9968.211.259973
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)
12.342.40.5080.761

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-VALUE2.3449.63859552296899.3910.1850.18380.2063Random selection43.243
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]
1.751-0.093-1.659
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_other_3_deg18.948
r_dihedral_angle_3_deg12.987
r_dihedral_angle_6_deg12.532
r_dihedral_angle_2_deg6.359
r_dihedral_angle_1_deg6.098
r_lrange_it5.334
r_lrange_other5.291
r_scangle_it3.253
r_scangle_other3.183
r_mcangle_it2.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_other_3_deg18.948
r_dihedral_angle_3_deg12.987
r_dihedral_angle_6_deg12.532
r_dihedral_angle_2_deg6.359
r_dihedral_angle_1_deg6.098
r_lrange_it5.334
r_lrange_other5.291
r_scangle_it3.253
r_scangle_other3.183
r_mcangle_it2.25
r_mcangle_other2.25
r_scbond_it2.032
r_scbond_other1.948
r_mcbond_it1.449
r_mcbond_other1.448
r_angle_refined_deg1.414
r_angle_other_deg0.496
r_nbd_refined0.213
r_symmetry_nbd_other0.192
r_nbtor_refined0.182
r_nbd_other0.18
r_symmetry_nbd_refined0.159
r_xyhbond_nbd_refined0.145
r_metal_ion_refined0.136
r_symmetry_xyhbond_nbd_refined0.122
r_symmetry_nbtor_other0.074
r_chiral_restr0.072
r_bond_refined_d0.006
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 Atoms9133
Nucleic Acid Atoms
Solvent Atoms476
Heterogen Atoms167

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing