7TIH | pdb_00007tih

Structure of oxidized bovine cytochrome c oxidase with reduced metal centers induced by synchrotron X-ray exposure


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7TIE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE6.8277PEG 4000, Potassium phosphate, Decylmaltoside
Crystal Properties
Matthews coefficientSolvent content
4.0869.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 178.037α = 90
b = 182.696β = 90
c = 205.854γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-07-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.9795SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.3539.33999.90.9936.76.9277487
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.352.480.4561

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7TIE2.3539.3392773741360399.8520.1950.1930.20.23510.2445.597
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]
-3.727-1.2084.935
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.334
r_dihedral_angle_3_deg16.705
r_dihedral_angle_4_deg14.652
r_lrange_other8.548
r_lrange_it8.546
r_dihedral_angle_other_3_deg7.212
r_dihedral_angle_1_deg6.837
r_scangle_it6.346
r_scangle_other6.346
r_mcangle_it4.896
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms28488
Nucleic Acid Atoms
Solvent Atoms1529
Heterogen Atoms2704

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing