5X19

CO bound cytochrome c oxidase at 100 micro sec after pump laser irradiation to release CO from O2 reduction center


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3AG1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE6.827740 mM sodium phosphate, 0.2% decyl maltoside, 2% ethylene glycol, PEG 4000
Crystal Properties
Matthews coefficientSolvent content
4.1970.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 185.034α = 90
b = 208.846β = 90
c = 178.046γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277CCDRAYONIX MX225HE2015-10-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSACLA BEAMLINE BL31.23970SACLABL3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.22596.90.16770.942911.7870.89336147
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2488.40.38120.59075.72

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3AG12.2253189141715696.760.17490.1730.2097RANDOM68.013
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]
0.582.75-3.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.493
r_dihedral_angle_3_deg17.805
r_dihedral_angle_4_deg17.107
r_dihedral_angle_1_deg6.37
r_angle_refined_deg1.975
r_chiral_restr0.126
r_bond_refined_d0.016
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms28506
Nucleic Acid Atoms
Solvent Atoms1415
Heterogen Atoms2256

Software

Software
Software NamePurpose
REFMACrefinement
cctbx.xfeldata processing
cctbx.primedata scaling
REFMACphasing