3FYE

Catalytic core subunits (I and II) of cytochrome c oxidase from Rhodobacter sphaeroides in the reduced state


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GSM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.327723-24% PEG-400, crystal reduced by dithionite, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.968.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.613α = 90
b = 131.472β = 90
c = 176.192γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2007-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.0332APS23-ID-B

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
12.125098.50.0664.6162159
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)
2.152.20692.70.606410331

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2GSM2.1550151414151414437599.090.1960.1960.1960.221RANDOM45.8
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]
-2.03-0.222.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.07
r_dihedral_angle_4_deg18.729
r_dihedral_angle_3_deg13.707
r_dihedral_angle_1_deg5.667
r_scangle_it2.042
r_scbond_it1.432
r_angle_refined_deg1.227
r_mcangle_it1.025
r_mcbond_it0.625
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.07
r_dihedral_angle_4_deg18.729
r_dihedral_angle_3_deg13.707
r_dihedral_angle_1_deg5.667
r_scangle_it2.042
r_scbond_it1.432
r_angle_refined_deg1.227
r_mcangle_it1.025
r_mcbond_it0.625
r_nbtor_refined0.31
r_symmetry_hbond_refined0.207
r_symmetry_vdw_refined0.203
r_nbd_refined0.196
r_metal_ion_refined0.127
r_xyhbond_nbd_refined0.123
r_chiral_restr0.088
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12452
Nucleic Acid Atoms
Solvent Atoms480
Heterogen Atoms679

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing