2H6D

Protein Kinase Domain of the Human 5'-AMP-activated protein kinase catalytic subunit alpha-2 (AMPK alpha-2 chain)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2FH9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	18.6% PEG 4000, 0.1M AmSO4, 0.1M Tris-HCl pH 8.5, 15%v/v isopropanol,5mM ATP/MgCl, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.454	α = 90
b = 67.41	β = 91.3
c = 50.493	γ = 90

Symmetry
Space Group	P 1 21 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	IMAGE PLATE	RIGAKU RAXIS IV		2006-05-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	1.85	19.72	98.8	0.047	26.91	3.5	22387	22387		-3

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)
	1.85	1.88	83		0.504	1.6	2.3	930

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	2FH9	1.85	19.72	22636	21209	1147	98.76	0.19003	0.18803	0.22674	RANDOM	28.52

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]
-0.7		-0.57	0.64		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.287
r_dihedral_angle_4_deg	16.364
r_dihedral_angle_3_deg	16.266
r_dihedral_angle_1_deg	5.501
r_scangle_it	5.356
r_scbond_it	3.926
r_mcangle_it	2.728
r_mcbond_it	1.997
r_angle_refined_deg	1.513
r_nbtor_refined	0.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.287
r_dihedral_angle_4_deg	16.364
r_dihedral_angle_3_deg	16.266
r_dihedral_angle_1_deg	5.501
r_scangle_it	5.356
r_scbond_it	3.926
r_mcangle_it	2.728
r_mcbond_it	1.997
r_angle_refined_deg	1.513
r_nbtor_refined	0.312
r_symmetry_vdw_refined	0.252
r_nbd_refined	0.22
r_xyhbond_nbd_refined	0.147
r_symmetry_hbond_refined	0.129
r_chiral_restr	0.12
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2068
Nucleic Acid Atoms
Solvent Atoms	164
Heterogen Atoms

Software

Software
Software Name	Purpose
SBC-Collect	data collection
HKL-2000	data reduction
PHASER	phasing
RESOLVE	model building
ARP/wARP	model building
REFMAC	refinement
HKL-2000	data scaling
RESOLVE	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.