3AQV

Human AMP-activated protein kinase alpha 2 subunit kinase domain (T172D) complexed with compound C


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YZAPDB ENTRY 2YZA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.92930.1M Bis-Tris (pH 6.5), 1.5M ammonium sulfate, 0.1M NaCl, 0.5mM Compound C, 5mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5752.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.476α = 90
b = 70.476β = 90
c = 130.508γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102007-06-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.000Photon FactoryAR-NW12A

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
12.085099.90.07234.212.120469-323
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)
12.082.191000.4098.14

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB ENTRY 2YZA2.082019340104499.870.224230.221330.28062RANDOM40.441
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]
0.330.33-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.66
r_dihedral_angle_3_deg18.307
r_dihedral_angle_4_deg17.958
r_dihedral_angle_1_deg6.364
r_scangle_it5.298
r_scbond_it3.393
r_mcangle_it2.311
r_angle_refined_deg2.071
r_mcbond_it1.35
r_chiral_restr0.163
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.66
r_dihedral_angle_3_deg18.307
r_dihedral_angle_4_deg17.958
r_dihedral_angle_1_deg6.364
r_scangle_it5.298
r_scbond_it3.393
r_mcangle_it2.311
r_angle_refined_deg2.071
r_mcbond_it1.35
r_chiral_restr0.163
r_bond_refined_d0.023
r_gen_planes_refined0.012
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 Atoms2159
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms30

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling