3OMI

Catalytic core subunits (I and II) of cytochrome C oxidase from Rhodobacter sphaeroides with D132A mutation


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.327726-29% PEG 400, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K, vapor diffusion, sitting drop
Crystal Properties
Matthews coefficientSolvent content
4.169.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.064α = 90
b = 131.519β = 90
c = 175.674γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2009-11-15SINGLE WEAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97872APS21-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
12.155097.30.092126.9151816
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)
12.152.2481.60.5565

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT2.1535.84151679457496.50.1930.1920.21538.49
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]
-1.61-0.371.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.208
r_dihedral_angle_4_deg18.227
r_dihedral_angle_3_deg13.436
r_dihedral_angle_1_deg5.54
r_scangle_it2.112
r_scbond_it1.484
r_angle_refined_deg1.164
r_mcangle_it1.072
r_mcbond_it0.657
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.208
r_dihedral_angle_4_deg18.227
r_dihedral_angle_3_deg13.436
r_dihedral_angle_1_deg5.54
r_scangle_it2.112
r_scbond_it1.484
r_angle_refined_deg1.164
r_mcangle_it1.072
r_mcbond_it0.657
r_nbtor_refined0.313
r_nbd_refined0.2
r_symmetry_vdw_refined0.182
r_xyhbond_nbd_refined0.139
r_metal_ion_refined0.121
r_chiral_restr0.084
r_symmetry_hbond_refined0.073
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12279
Nucleic Acid Atoms
Solvent Atoms491
Heterogen Atoms646

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MD2data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing