6YNT

Crystal structure of the cAMP-dependent protein kinase A in complex with aminofasudil and PKI (5-24)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6F14 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.92770.2 mM PKA , 100 mM MBT (MES/Bis-Tris Puffer pH 6.9), 1 mM DTT, 0.1 mM EDTA, 75 mM LiCl, 0.2 mM Mega8, 0.5 mM PKI, 16-23% (v/v) Methanol. Soaking in buffer with 10% (v/v) of aminofasudil (50mM stock) in DMSO and 30% (v/v) MPD
Crystal Properties
Matthews coefficientSolvent content
2.6453.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.524α = 90
b = 74.46β = 90
c = 80.359γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-07-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918400BESSY14.1

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
11.5243.6399.50.04417.084.46731620.29
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)
11.521.6199.60.442.97

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-VALUE6F141.5243.631.3767315336699.550.17050.16940.191426.59
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_d21.7767
f_angle_d0.9714
f_chiral_restr0.0555
f_bond_d0.0076
f_plane_restr0.0071
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2881
Nucleic Acid Atoms
Solvent Atoms270
Heterogen Atoms53

Software

Software
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling
Cootmodel building