8H8R

Bovine Heart Cytochrome c Oxidase in the Calcium-bound Fully Oxidized State


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7COH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE6.827740 mM sodium phosphate buffer, pH 6.8 0.2% (w/v) decyl-maltoside 1% (w/v) polyethylene glycol 4000
Crystal Properties
Matthews coefficientSolvent content
4.0869.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 182.8α = 90
b = 205.7β = 90
c = 177.9γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90PIXELDECTRIS EIGER X 16M2018-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)CC (Half)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
11.720099.80.0850.99714.18.769121932.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7497.91.380.781.68.4

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 REPLACEMENTTHROUGHOUT7COH1.7406912193610999.970.124190.122650.15306RANDOM42.188
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]
-1.792.65-0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.744
r_dihedral_angle_4_deg15.598
r_dihedral_angle_3_deg13.887
r_scangle_other7.38
r_long_range_B_refined6.696
r_long_range_B_other6.625
r_scbond_it6.569
r_scbond_other6.569
r_dihedral_angle_1_deg6.073
r_mcangle_it4.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.744
r_dihedral_angle_4_deg15.598
r_dihedral_angle_3_deg13.887
r_scangle_other7.38
r_long_range_B_refined6.696
r_long_range_B_other6.625
r_scbond_it6.569
r_scbond_other6.569
r_dihedral_angle_1_deg6.073
r_mcangle_it4.62
r_mcangle_other4.62
r_mcbond_it4.095
r_mcbond_other4.092
r_rigid_bond_restr3.864
r_angle_refined_deg1.841
r_angle_other_deg1.459
r_chiral_restr0.452
r_bond_refined_d0.016
r_gen_planes_refined0.01
r_gen_planes_other0.005
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms27834
Nucleic Acid Atoms
Solvent Atoms2007
Heterogen Atoms2590

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing