9FIJ

Crystal Structure of reduced NuoEF variant E222K(NuoF) from Aquifex aeolicus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 9FIIRfree flags were transferred from scaled data of isomorphous crystal structure 9FII followed by direct Fourier synthesis using 9FII as starting model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.12810.1 M Tris pH 7.1, 0.85 M Na3-citrate, 0.1 M NaCl
Crystal Properties
Matthews coefficientSolvent content
2.5651.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.984α = 90
b = 113.438β = 90
c = 189.11γ = 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
12.3548.68799.90.0770.9967.46.458277
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)
12.352.410.4360.857

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 DIFFRACTIONFOURIER SYNTHESISFREE R-VALUE2.3548.68758200285399.9160.1950.19310.2363Rfree flags were transferred from scaled data of isomorphous structure (pdb ID 9FII)36.69
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]
0.9011.474-2.375
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.146
r_dihedral_angle_other_3_deg12.631
r_dihedral_angle_6_deg12.598
r_dihedral_angle_1_deg5.861
r_dihedral_angle_2_deg5.787
r_lrange_it4.485
r_lrange_other4.448
r_scangle_it2.399
r_scangle_other2.382
r_mcangle_other1.753
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.146
r_dihedral_angle_other_3_deg12.631
r_dihedral_angle_6_deg12.598
r_dihedral_angle_1_deg5.861
r_dihedral_angle_2_deg5.787
r_lrange_it4.485
r_lrange_other4.448
r_scangle_it2.399
r_scangle_other2.382
r_mcangle_other1.753
r_mcangle_it1.752
r_scbond_it1.444
r_scbond_other1.415
r_angle_refined_deg1.296
r_mcbond_it1.055
r_mcbond_other1.054
r_angle_other_deg0.462
r_symmetry_nbd_refined0.274
r_nbd_other0.226
r_nbd_refined0.204
r_symmetry_nbd_other0.193
r_nbtor_refined0.181
r_xyhbond_nbd_refined0.141
r_metal_ion_refined0.135
r_symmetry_xyhbond_nbd_refined0.086
r_symmetry_nbtor_other0.075
r_chiral_restr0.066
r_symmetry_xyhbond_nbd_other0.054
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9040
Nucleic Acid Atoms
Solvent Atoms403
Heterogen Atoms130

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing