8EM8

Co-crystal structure of the cGMP-dependent protein kinase PKG from Plasmodium falciparum in complex with RY-1-165

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	20% PEG3350, 0.2M KCL

Crystal Properties
Matthews coefficient	Solvent content
3.31	62.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.145	α = 90
b = 127.986	β = 90
c = 213.728	γ = 90

Symmetry
Space Group	C 2 2 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 EIGER X 16M		2021-04-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.97918	APS	24-ID-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.54	50	99.4	0.118	0.135	0.064	7.8	4.1		44070

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.54	2.58	99.5		0.972	1.131	0.568	0.479		3.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5DYK	2.54	47.65	41028	2135	99.4	0.2205	0.2183	0.2626	RANDOM	42.523

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]
-2.61			0.45		2.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.593
r_dihedral_angle_4_deg	18.559
r_dihedral_angle_3_deg	16.26
r_dihedral_angle_1_deg	7.614
r_angle_refined_deg	1.202
r_angle_other_deg	1.169
r_chiral_restr	0.043
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.593
r_dihedral_angle_4_deg	18.559
r_dihedral_angle_3_deg	16.26
r_dihedral_angle_1_deg	7.614
r_angle_refined_deg	1.202
r_angle_other_deg	1.169
r_chiral_restr	0.043
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5917
Nucleic Acid Atoms
Solvent Atoms	152
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

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 R01GM133198.