6YQI

Crystal structure of cAMP-dependent Protein Kinase (PKA) in complex with long-chain Fasudil-derivative N-[2-(propylamino)ethyl]isoquinoline-5-sulfonamide (soaked)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Q8W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.9	277	0.24mM 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 coefficient	Solvent content
2.79	55.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.107	α = 90
b = 72.482	β = 90
c = 108.739	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2013-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.918409	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.417	45.337	98.5	0.038	22.72	6.7		86529			18.15

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.42	1.5			0.462	3.12

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1Q8W	1.42	36.24	1.36	86523	4326	98.52	0.155	0.1537	0.1801	27.6

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
Key	Refinement Restraint Deviation
f_dihedral_angle_d	20.0939
f_angle_d	0.9292
f_chiral_restr	0.071
f_bond_d	0.0067
f_plane_restr	0.0066

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2832
Nucleic Acid Atoms
Solvent Atoms	296
Heterogen Atoms	20

Software

Software
Software Name	Purpose
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling
Coot	model building

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.