6MYU

Avian mitochondrial complex II crystallized in the presence of HQNO


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.527748 g/L PEG3350, 15 mL/L PEG400, 24 mL/L isopropanol, 0.05 M HEPES sodium, 0.01 M Tris-HCl, 1.6 mM manganese chloride, 0.64 mM magnesium chloride, 1.5 mM sodium azide, 0.25 mM sodium EDTA, 10 g/L octyl beta-D-glucoside, undecyl-beta-D-maltoside, |HQNO
Crystal Properties
Matthews coefficientSolvent content
3.4664.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.029α = 90
b = 83.958β = 90
c = 290.54γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2004-10-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.20.9743ALS8.2.2

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
11.9747.7899.70.1048.36.3812171533.79
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)
11.972.0399.41.4331.25.52

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 1YQ31.9747.781.33121673246199.70.1990.1990.223Random selection50.381
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_d10.909
f_angle_d0.922
f_chiral_restr0.051
f_bond_d0.007
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8491
Nucleic Acid Atoms
Solvent Atoms431
Heterogen Atoms489

Software

Software
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing