3DTU

Catalytic core subunits (I and II) of cytochrome c oxidase from Rhodobacter sphaeroides complexed with deoxycholic acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.327724% PEG-400, 5mM deoxycholic acid , pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.6966.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.243α = 90
b = 132.052β = 90
c = 167.966γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2007-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.9785APS21-ID-G

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
12.155096.80.06921.96.6150058145257
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)
2.152.3377.60.5132.13.811510

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 DIFFRACTIONTHROUGHOUTPDB entry 2GSM2.1540148964144361361296.910.1840.1840.1840.212RANDOM38.516
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]
-1.73-0.822.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.681
r_dihedral_angle_4_deg16.208
r_dihedral_angle_3_deg13.853
r_dihedral_angle_1_deg5.681
r_scangle_it1.965
r_scbond_it1.376
r_angle_refined_deg1.215
r_mcangle_it0.983
r_mcbond_it0.594
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.681
r_dihedral_angle_4_deg16.208
r_dihedral_angle_3_deg13.853
r_dihedral_angle_1_deg5.681
r_scangle_it1.965
r_scbond_it1.376
r_angle_refined_deg1.215
r_mcangle_it0.983
r_mcbond_it0.594
r_nbtor_refined0.312
r_symmetry_vdw_refined0.201
r_nbd_refined0.199
r_xyhbond_nbd_refined0.127
r_metal_ion_refined0.108
r_chiral_restr0.088
r_symmetry_hbond_refined0.072
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12565
Nucleic Acid Atoms
Solvent Atoms636
Heterogen Atoms780

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
PHASERphasing