7D5W

Bovine heart cytochrome c oxidase in a catalytic intermediate of O at 1.84 angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE6.7277PEG 4000, SODIUM PHOSPHATE BUFFER
Crystal Properties
Matthews coefficientSolvent content
4.0469.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 181.435α = 90
b = 203.092β = 90
c = 177.794γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray50CCDRAYONIX MX-2252015-02-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.90SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.8413799.80.0960.03331.77.3561788
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.841.8699.80.8960.44.45.8

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5B1A1.8439.9151.335613062827999.750.15550.1540.184
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_d17.696
f_angle_d1.447
f_chiral_restr0.083
f_bond_d0.015
f_plane_restr0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms28437
Nucleic Acid Atoms
Solvent Atoms2992
Heterogen Atoms2514

Software

Software
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
HKL-2000data scaling
DMphasing