3OMA

Catalytic core subunits (I and II) of cytochrome C oxidase from Rhodobacter sphaeroides with K362M mutation


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.327726-28% PEG-400, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K, vapor diffusion, sitting drop
Crystal Properties
Matthews coefficientSolvent content
4.1270.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.019α = 90
b = 131.579β = 90
c = 176.626γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2008-07-12SINGLE WEAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G1.0APS21-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
12.1550920.05913.85.5145094
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)
12.152.2357.60.49739013

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.350122612126383377197.570.19220.19140.219RANDOM47.1316
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]
-2.460.412.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.688
r_dihedral_angle_4_deg19.866
r_dihedral_angle_3_deg14.135
r_dihedral_angle_1_deg5.653
r_scangle_it1.931
r_scbond_it1.317
r_angle_refined_deg1.185
r_mcangle_it1.006
r_mcbond_it0.592
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.688
r_dihedral_angle_4_deg19.866
r_dihedral_angle_3_deg14.135
r_dihedral_angle_1_deg5.653
r_scangle_it1.931
r_scbond_it1.317
r_angle_refined_deg1.185
r_mcangle_it1.006
r_mcbond_it0.592
r_nbtor_refined0.311
r_nbd_refined0.198
r_symmetry_vdw_refined0.172
r_xyhbond_nbd_refined0.138
r_symmetry_hbond_refined0.117
r_metal_ion_refined0.107
r_chiral_restr0.087
r_bond_refined_d0.011
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12297
Nucleic Acid Atoms
Solvent Atoms452
Heterogen Atoms646

Software

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