3HB3

High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AR1PDB entry 1AR1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.527725% glycerol, pH 5.5, VAPOR DIFFUSION, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
4.0269.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.403α = 90
b = 150.473β = 90
c = 157.185γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2005-10-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9198SLSX10SA

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
12.25111.899.040.12414.24.99070990709-3-3
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)
2.252.3298.30.3793.24.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUTPDB entry 1AR12.2519.98-39070990709281999.040.220240.220240.218360.27996RANDOM45.272
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
r_dihedral_angle_1_deg8.795
r_scangle_it5.166
r_scbond_it3.538
r_angle_refined_deg2.683
r_mcangle_it2.407
r_mcbond_it1.381
r_symmetry_vdw_refined0.323
r_symmetry_hbond_refined0.313
r_nbd_refined0.264
r_xyhbond_nbd_refined0.234
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.795
r_scangle_it5.166
r_scbond_it3.538
r_angle_refined_deg2.683
r_mcangle_it2.407
r_mcbond_it1.381
r_symmetry_vdw_refined0.323
r_symmetry_hbond_refined0.313
r_nbd_refined0.264
r_xyhbond_nbd_refined0.234
r_chiral_restr0.23
r_bond_refined_d0.031
r_gen_planes_refined0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7956
Nucleic Acid Atoms
Solvent Atoms554
Heterogen Atoms883

Software

Software
Software NamePurpose
MAR345dtbdata collection
EPMRphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling