5XDQ

Bovine heart cytochrome c oxidase in the fully oxidized state with pH 7.3 at 1.77 angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1V54 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE7.32773% polythylene glycol (PEG), 0.35% decal maltose, 0.70% fluorinated octyl-maltoside, 33mM sodium acetate, 25mM Tris-HCL (pH 7.3)

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 183.307α = 90
b = 205.904β = 90
c = 177.526γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray50CCDRAYONIX MX-2252014-07-09MSINGLE 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)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
11.7720099.90.086138.9643861
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.771.791008.216039

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 REPLACEMENTTHROUGHOUT1V541.77134.4536110173236199.590.16520.16390.1904RANDOM45.057
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]
-0.296.37-6.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.805
r_sphericity_free25.121
r_sphericity_bonded23.645
r_dihedral_angle_3_deg13.76
r_dihedral_angle_4_deg13.607
r_dihedral_angle_1_deg5.164
r_rigid_bond_restr2.409
r_angle_refined_deg1.203
r_chiral_restr0.082
r_gen_planes_refined0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.805
r_sphericity_free25.121
r_sphericity_bonded23.645
r_dihedral_angle_3_deg13.76
r_dihedral_angle_4_deg13.607
r_dihedral_angle_1_deg5.164
r_rigid_bond_restr2.409
r_angle_refined_deg1.203
r_chiral_restr0.082
r_gen_planes_refined0.02
r_bond_refined_d0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms28442
Nucleic Acid Atoms
Solvent Atoms2883
Heterogen Atoms2542

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
MOLREPphasing