9FDK

Crystal Structure of oxidized NuoEF variant R66G(NuoF) from Aquifex aeolicus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 9FDJRfree flags transferred from isomorphous data set of NuoEF_R66G

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.32810.1 M BisTris pH 6.3, 1.4 M ammonium sulfate, 100 mM NaCl
Crystal Properties
Matthews coefficientSolvent content
2.652.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.283α = 90
b = 116.318β = 90
c = 189.318γ = 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
11.863.399.90.0420.998116.3130020
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)
11.81.830.4560.7871.9

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-VALUE1.860.091129899658399.820.1570.15580.1864Random selection27.098
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]
0.1841.248-1.432
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.678
r_dihedral_angle_other_3_deg13.015
r_dihedral_angle_3_deg11.567
r_dihedral_angle_2_deg6.741
r_dihedral_angle_1_deg5.985
r_lrange_it5.17
r_lrange_other5.055
r_scangle_it3.221
r_scangle_other3.136
r_scbond_it2.018
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.678
r_dihedral_angle_other_3_deg13.015
r_dihedral_angle_3_deg11.567
r_dihedral_angle_2_deg6.741
r_dihedral_angle_1_deg5.985
r_lrange_it5.17
r_lrange_other5.055
r_scangle_it3.221
r_scangle_other3.136
r_scbond_it2.018
r_scbond_other1.951
r_mcangle_it1.547
r_mcangle_other1.547
r_angle_refined_deg1.434
r_mcbond_it1.048
r_mcbond_other1.045
r_angle_other_deg0.498
r_metal_ion_refined0.275
r_symmetry_xyhbond_nbd_refined0.221
r_nbd_refined0.215
r_nbd_other0.186
r_symmetry_nbd_other0.185
r_nbtor_refined0.182
r_symmetry_nbd_refined0.173
r_xyhbond_nbd_refined0.147
r_xyhbond_nbd_other0.121
r_symmetry_nbtor_other0.074
r_chiral_restr0.073
r_chiral_restr_other0.031
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9103
Nucleic Acid Atoms
Solvent Atoms886
Heterogen Atoms173

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing