7LCB

C1B domain of Protein kinase C in complex with prostratin and phosphatidylcholine


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; Prostratin: 2.5 mM
Crystal Properties
Matthews coefficientSolvent content
2.141.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.402α = 90
b = 25.869β = 97.29
c = 57.964γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120PIXELBruker PHOTON II2020-09-14MSINGLE 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
11.744.689.10.055815.483.855115
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)
11.71.848.40.26363

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 REPLACEMENTTHROUGHOUT1ptq1.728.751.36511324389.120.1740.17190.213617.4806
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_d44.539
f_angle_d1.445
f_chiral_restr0.089
f_bond_d0.009
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms417
Nucleic Acid Atoms
Solvent Atoms38
Heterogen Atoms62

Software

Software
Software NamePurpose
PHENIXrefinement
SAINTdata reduction
SAINTdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing