3MN3

An inhibited conformation for the protein kinase domain of the Saccharomyces cerevisiae AMPK homolog Snf1

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	294	10% (w/v) PEG3350 and 50mM Na2SO4, pH 7.5, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3.42	64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.981	α = 90
b = 76.981	β = 90
c = 286.215	γ = 90

Symmetry
Space Group	I 41 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate		2009-04-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4C	0.9815	NSLS	X4C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.38	30	99			19910	19799	3	3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.38	2.48	99

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.38	30	17349	872	98.97	0.231	0.23	0.246	RANDOM	59.94

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]
2.88			2.88		-5.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.142
r_dihedral_angle_4_deg	21.35
r_dihedral_angle_3_deg	16.76
r_dihedral_angle_1_deg	5.605
r_scangle_it	2.105
r_scbond_it	1.293
r_angle_refined_deg	1.27
r_mcangle_it	1.133
r_mcbond_it	0.615
r_nbtor_refined	0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.142
r_dihedral_angle_4_deg	21.35
r_dihedral_angle_3_deg	16.76
r_dihedral_angle_1_deg	5.605
r_scangle_it	2.105
r_scbond_it	1.293
r_angle_refined_deg	1.27
r_mcangle_it	1.133
r_mcbond_it	0.615
r_nbtor_refined	0.305
r_symmetry_vdw_refined	0.211
r_symmetry_hbond_refined	0.211
r_nbd_refined	0.196
r_xyhbond_nbd_refined	0.13
r_chiral_restr	0.08
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2040
Nucleic Acid Atoms
Solvent Atoms	54
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling
COMO	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.