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)
TypeSourceAccession CodeDetails
experimental modelPDB 2FH9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529818.6% 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 coefficientSolvent content
2.1342.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.454α = 90
b = 67.41β = 91.3
c = 50.493γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2006-05-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.8519.7298.80.04726.913.52238722387-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.851.88830.5041.62.3930

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2FH91.8519.722263621209114798.760.190030.188030.22674RANDOM28.52
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]
-0.7-0.570.640.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.287
r_dihedral_angle_4_deg16.364
r_dihedral_angle_3_deg16.266
r_dihedral_angle_1_deg5.501
r_scangle_it5.356
r_scbond_it3.926
r_mcangle_it2.728
r_mcbond_it1.997
r_angle_refined_deg1.513
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.287
r_dihedral_angle_4_deg16.364
r_dihedral_angle_3_deg16.266
r_dihedral_angle_1_deg5.501
r_scangle_it5.356
r_scbond_it3.926
r_mcangle_it2.728
r_mcbond_it1.997
r_angle_refined_deg1.513
r_nbtor_refined0.312
r_symmetry_vdw_refined0.252
r_nbd_refined0.22
r_xyhbond_nbd_refined0.147
r_symmetry_hbond_refined0.129
r_chiral_restr0.12
r_bond_refined_d0.015
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2068
Nucleic Acid Atoms
Solvent Atoms164
Heterogen Atoms

Software

Software
Software NamePurpose
SBC-Collectdata collection
HKL-2000data reduction
PHASERphasing
RESOLVEmodel building
ARP/wARPmodel building
REFMACrefinement
HKL-2000data scaling
RESOLVEphasing