5DZC

Crystal structure of the cGMP-dependent protein kinase PKG from Plasmodium Vivax - AMPPNP bound

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4MYI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	18.2% PEG3350, 0.1 M HEPES pH 7.0, 0.1M Succinate, 2mM MgCl2,5mM AMPPNP

Crystal Properties
Matthews coefficient	Solvent content
3.97	69.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 193.111	α = 90
b = 117.906	β = 95.08
c = 67.731	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315		2015-04-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97929	APS	19-ID

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	2.3	50	99.1	0.09	0.104	0.05	7	4.1		65835

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	2.3	2.38	95.5		0.845	0.973	0.475	0.698		3.7	6286

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	FOURIER SYNTHESIS	THROUGHOUT	4MYI	2.3	50	62646	3186	98.42	0.2228	0.2212	0.255	RANDOM	74.39

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]
1.85		0.15	-4.14		2.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.736
r_dihedral_angle_4_deg	14.494
r_dihedral_angle_3_deg	13.706
r_dihedral_angle_1_deg	5.906
r_mcangle_it	1.487
r_angle_refined_deg	1.361
r_angle_other_deg	0.917
r_mcbond_it	0.811
r_mcbond_other	0.811
r_chiral_restr	0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.736
r_dihedral_angle_4_deg	14.494
r_dihedral_angle_3_deg	13.706
r_dihedral_angle_1_deg	5.906
r_mcangle_it	1.487
r_angle_refined_deg	1.361
r_angle_other_deg	0.917
r_mcbond_it	0.811
r_mcbond_other	0.811
r_chiral_restr	0.08
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6395
Nucleic Acid Atoms
Solvent Atoms	144
Heterogen Atoms	42

Software

Software
Software Name	Purpose
HKL-3000	data collection
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
REFMAC	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 R01GM157729.