6YNC

Crystal structure of cAMP-dependent Protein Kinase (PKA) in complex with the methylated Fasudil-derived fragment N-methylisoquinoline-5-sulfonamide (soaked)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Q8W 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.92770.24mM PKA, 30mM MBT (MES/Bis-Tris Buffer pH 6.2-6.9), 1mM DTT, 0.1mM EDTA, 75mM LiCl, 0.3mM Mega 8, 0.7mM PKI, 16%(v/v) methanol; soaking in buffer described with 0.12mM ligand solved in DMSO and 30%(v/v) MPD
Crystal Properties
Matthews coefficientSolvent content
2.856.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.285α = 90
b = 73.122β = 90
c = 109.348γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918409BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.39645.57797.90.04919.016.79142215.13
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4893.70.4673.03

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 REPLACEMENTFREE R-VALUE1Q8W1.436.561.3691419457197.910.14980.14860.172923.04
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_d21.4815
f_angle_d0.9638
f_chiral_restr0.0748
f_bond_d0.0074
f_plane_restr0.0068
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2884
Nucleic Acid Atoms
Solvent Atoms372
Heterogen Atoms15

Software

Software
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling
Cootmodel building