2YZA

Crystal structure of kinase domain of Human 5'-AMP-activated protein kinase alpha-2 subunit mutant (T172D)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2H6DPDB ENTRY 2H6D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.92930.1M Tris-HCl pH8.9, 16% PEG4000, 15% isopropanol, 0.1M Ammonium sulfate, Protein solution: 5mM AMPPNP, 5mM Magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1141.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.187α = 90
b = 67.336β = 91.26
c = 50.651γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 210rhodium coated mirror2006-09-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B21.000SPring-8BL26B2

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
132594.30.10611.53491348.3
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)
133.0551.60.2513.21.7126

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 2H6D3.0225442248493.310.2350.2270.308RANDOM21.753
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]
0.990.510.15-1.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.402
r_dihedral_angle_3_deg15.713
r_dihedral_angle_4_deg13.511
r_dihedral_angle_1_deg4.405
r_angle_refined_deg0.873
r_scangle_it0.444
r_mcangle_it0.315
r_nbtor_refined0.295
r_scbond_it0.26
r_mcbond_it0.177
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.402
r_dihedral_angle_3_deg15.713
r_dihedral_angle_4_deg13.511
r_dihedral_angle_1_deg4.405
r_angle_refined_deg0.873
r_scangle_it0.444
r_mcangle_it0.315
r_nbtor_refined0.295
r_scbond_it0.26
r_mcbond_it0.177
r_symmetry_vdw_refined0.168
r_nbd_refined0.166
r_xyhbond_nbd_refined0.092
r_symmetry_hbond_refined0.086
r_chiral_restr0.055
r_bond_refined_d0.006
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms2063
Nucleic Acid Atoms
Solvent Atoms10
Heterogen Atoms

Software

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