9FE7

Crystal Structure of oxidized 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 to fill 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
2.652.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.283α = 90
b = 116.13β = 90
c = 189.842γ = 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
12.2848.001980.0890.9825.7463251
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)
12.282.340.3230.797

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-VALUE2.2848.00162976316097.2930.20.19750.2443Random selection23.267
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]
-1.1862.524-1.337
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_other_3_deg15.306
r_dihedral_angle_6_deg13.485
r_dihedral_angle_3_deg12.908
r_dihedral_angle_2_deg8.235
r_dihedral_angle_1_deg6.429
r_lrange_it3.094
r_lrange_other2.905
r_angle_refined_deg1.463
r_scangle_it1.32
r_scangle_other1.269
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_other_3_deg15.306
r_dihedral_angle_6_deg13.485
r_dihedral_angle_3_deg12.908
r_dihedral_angle_2_deg8.235
r_dihedral_angle_1_deg6.429
r_lrange_it3.094
r_lrange_other2.905
r_angle_refined_deg1.463
r_scangle_it1.32
r_scangle_other1.269
r_scbond_it0.844
r_mcangle_it0.796
r_mcangle_other0.796
r_scbond_other0.794
r_angle_other_deg0.513
r_mcbond_it0.472
r_mcbond_other0.472
r_nbd_refined0.217
r_symmetry_nbd_refined0.208
r_symmetry_nbd_other0.191
r_symmetry_xyhbond_nbd_refined0.19
r_nbtor_refined0.183
r_nbd_other0.167
r_xyhbond_nbd_refined0.163
r_metal_ion_refined0.136
r_symmetry_xyhbond_nbd_other0.078
r_chiral_restr0.075
r_symmetry_nbtor_other0.074
r_chiral_restr_other0.018
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 Atoms9089
Nucleic Acid Atoms
Solvent Atoms726
Heterogen Atoms161

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing