5B3S

Bovine heart cytochrome c oxidase in the carbon monoxide-bound mixed-valence state at 1.68 angstrom resolution (50 K)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5B1A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE6.827740mM Sodium phosphate, 0.2% decylmaltoside, 2% EG, PEG 4000
Crystal Properties
Matthews coefficientSolvent content
4.0669.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 181.491α = 90
b = 203.303β = 90
c = 177.484γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray50CCDRAYONIX MX300HE2013-06-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.6820099.90.090.0940.0289.710.2737777
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)
11.681.691001.1321.2010.3970.8328.9

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 REPLACEMENTTHROUGHOUT5B1A1.6839.6241.337364373702599.840.15380.15260.1771RANDOM
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_d18.524
f_angle_d1.722
f_chiral_restr0.099
f_bond_d0.015
f_plane_restr0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms28449
Nucleic Acid Atoms
Solvent Atoms2829
Heterogen Atoms3148

Software

Software
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
DENZOdata reduction
REFMACphasing
PDB_EXTRACTdata extraction