6R7P

Crystal structure of oxidized Aquifex aeolicus NADH-quinone oxidoreductase subunits NuoE and NuoF S96M


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6Q9K 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION6.5289(NH4)2SO4, BisTris, NaCl, cryo-protection with glycerol
Crystal Properties
Matthews coefficientSolvent content
2.6453.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.41α = 90
b = 114.64β = 90
c = 187.87γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2019-03-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54187

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
13.2238.2199.80.2690.2910.110.9916.86.722909
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.223.481000.890.9640.3670.7956.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6Q9K3.2231.7321749111299.630.21040.20790.2572RANDOM60.227
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]
-1.662.43-0.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.807
r_dihedral_angle_3_deg16.177
r_dihedral_angle_4_deg12.914
r_dihedral_angle_1_deg6.673
r_angle_refined_deg1.321
r_angle_other_deg1.121
r_chiral_restr0.053
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.807
r_dihedral_angle_3_deg16.177
r_dihedral_angle_4_deg12.914
r_dihedral_angle_1_deg6.673
r_angle_refined_deg1.321
r_angle_other_deg1.121
r_chiral_restr0.053
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 Atoms9104
Nucleic Acid Atoms
Solvent Atoms111
Heterogen Atoms101

Software

Software
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing