3TDH

Structure of the regulatory fragment of sccharomyces cerevisiae AMPK in complex with AMP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72911M succinic Acid, 0.1M HEPES, 1% w/v Polyethylene glycol monomethyl ether 2000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
3.2662.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.97α = 90
b = 242.378β = 90
c = 79.352γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9763DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.33099.563888538885-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.42397.33

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.32538885206299.560.250340.248210.29013RANDOM47.11
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]
1.520.29-1.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.13
r_dihedral_angle_4_deg17.244
r_dihedral_angle_3_deg15.37
r_dihedral_angle_1_deg4.533
r_scangle_it1.526
r_angle_refined_deg0.956
r_mcangle_it0.875
r_scbond_it0.861
r_mcbond_it0.474
r_chiral_restr0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.13
r_dihedral_angle_4_deg17.244
r_dihedral_angle_3_deg15.37
r_dihedral_angle_1_deg4.533
r_scangle_it1.526
r_angle_refined_deg0.956
r_mcangle_it0.875
r_scbond_it0.861
r_mcbond_it0.474
r_chiral_restr0.06
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4408
Nucleic Acid Atoms
Solvent Atoms168
Heterogen Atoms23

Software

Software
Software NamePurpose
GDAdata collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling