1AR1

Structure at 2.7 Angstrom Resolution of the Paracoccus Denitrificans two-subunit Cytochrome C Oxidase Complexed with an Antibody Fv Fragment


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherFOUR PROTEIN SUBUNITS CONTAINING CYTOCHROME C OXIDASE FROM PARACOCCUS DENITRIFICANS (NATURE 376: 660-669)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.5pH 5.5
Crystal Properties
Matthews coefficientSolvent content
4.872

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.5α = 90
b = 151β = 90
c = 156.7γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277CCDPRINCETON 2KCOLLIMATING AND FOCUSSING MIRROR1997-01-31M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
12.75093.80.06813.43.45737344.2
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)
2.72.879.70.33242.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTFOUR PROTEIN SUBUNITS CONTAINING CYTOCHROME C OXIDASE FROM PARACOCCUS DENITRIFICANS (NATURE 376: 660-669)2.730257373291093.10.2070.2070.261RANDOM59.7
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]
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d23.4
x_scangle_it6.44
x_mcangle_it5.08
x_scbond_it4.53
x_mcbond_it3.18
x_improper_angle_d2.47
x_angle_deg1.6
x_bond_d0.012
x_bond_d_na
x_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d23.4
x_scangle_it6.44
x_mcangle_it5.08
x_scbond_it4.53
x_mcbond_it3.18
x_improper_angle_d2.47
x_angle_deg1.6
x_bond_d0.012
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7926
Nucleic Acid Atoms
Solvent Atoms52
Heterogen Atoms266

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing