6MYS

Avian mitochondrial complex II with Atpenin A5 bound, sidechain outside


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YQ3PDB ENTRY 1YQ3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.527747 g/L PEG3350, 30 mL/L PEG400, 23 mL/L isopropanol, 0.05 M HEPES sodium, 0.01 M Tris-HCl, 3.1 mM manganese chloride, 0.62 mM magnesium chloride, 1.5 mM sodium azide, 0.25 mM sodium EDTA, 10 g/L octyl beta-D-glucoside, undecyl-beta-D-maltoside, crystal was soaked with Atpenin A5 after crystallization
Crystal Properties
Matthews coefficientSolvent content
3.665.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.68α = 90
b = 84.424β = 90
c = 293.019γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2007-02-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.21.000ALS8.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.3738.8399.70.1567.79.077399644.58
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.372.4499.41.1161.77.97

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEPDB ENTRY 1YQ32.3738.751.3372805214499.30.2120.2110.237random74.4621
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d10.013
f_angle_d0.547
f_chiral_restr0.039
f_plane_restr0.003
f_bond_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8494
Nucleic Acid Atoms
Solvent Atoms123
Heterogen Atoms379

Software

Software
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing