6RSX | pdb_00006rsx

Regulatory Subunit of cAMP-dependant Protein Kinase A from Euglena gracilis at 1.6 A resolution

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277.15	1) 50mM MES pH 6.0 , 4% MPD , 80mM Ammonium sulfate , 18% PEG 8000 2) 50mM MES pH 6.0, 20% PEG 3350 3) 50mM MES pH 6.0 , 4% MPD , 0.2M Ammonium sulfate , 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.13	60.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.586	α = 90
b = 80.586	β = 90
c = 110.755	γ = 120

Symmetry
Space Group	P 61

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 2M		2017-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.000	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.6	69.79	99.6	0.073	0.999	14.33	10.1	104899	52962			34.7817722306

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.69			0.08069	0.0851	0.483

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1RGS	1.6	69.79	1.33057047932	52599	5067	99.0867057534	0.193489922461	0.192252314238	0.19	0.216302265951	0.22	45.5093514939

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	17.2829177784
f_angle_d	1.08436789528
f_chiral_restr	0.0760290362523
f_bond_d	0.0110016187995
f_plane_restr	0.00656436908538

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2094
Nucleic Acid Atoms
Solvent Atoms	159
Heterogen Atoms	44

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHASER	phasing
Aimless	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.