7KO6

C1B domain of Protein kinase C in complex with ingenol-3-angelate and phosphocholine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PTQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5277.15Screen condition: 0.2 M Ammonium acetate, 0.1 M Sodium phosphate, 30% Isopropanol, pH 6.8, Drop condition: Protein: 2 mM in MES pH 6.5, 150 mM KCl, Phosphatidylcholine: 20 mM, Ingenol-3-angelate: 2.5 mM
Crystal Properties
Matthews coefficientSolvent content
2.0941.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.384α = 90
b = 25.909β = 98.39
c = 57.731γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120PIXELBruker PHOTON II2020-09-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54

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
11.8571000.114415.7612.544819
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)
11.81.91000.483.79

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1ptq1.828.561.35481525899.810.17790.17570.215418.5386
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
f_dihedral_angle_d41.937
f_angle_d2.187
f_chiral_restr0.095
f_bond_d0.011
f_plane_restr0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms417
Nucleic Acid Atoms
Solvent Atoms53
Heterogen Atoms65

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SAINTdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing