3E8D

Crystal structures of the kinase domain of AKT2 in complex with ATP-competitive inhibitors


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION829814% PEG 2KMME, 100 mM Tris pH 8.0 and 10% ethanol diffused in. Seeded., vapor diffusion, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2144.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.823α = 90
b = 116.823β = 90
c = 45.102γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210un-focused beam2005-10-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.000APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.741.21000.2335.7188732
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.81000.825

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 DIFFRACTIONTHROUGHOUT2.741.21789197199.990.213660.210820.26775RANDOM22.852
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]
0.190.090.19-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.179
r_dihedral_angle_4_deg14.084
r_dihedral_angle_3_deg13.503
r_dihedral_angle_1_deg5.185
r_angle_refined_deg1.16
r_angle_other_deg0.768
r_scangle_it0.647
r_scbond_it0.378
r_mcangle_it0.376
r_symmetry_vdw_other0.214
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.179
r_dihedral_angle_4_deg14.084
r_dihedral_angle_3_deg13.503
r_dihedral_angle_1_deg5.185
r_angle_refined_deg1.16
r_angle_other_deg0.768
r_scangle_it0.647
r_scbond_it0.378
r_mcangle_it0.376
r_symmetry_vdw_other0.214
r_mcbond_it0.212
r_nbd_refined0.183
r_nbtor_refined0.175
r_nbd_other0.172
r_xyhbond_nbd_refined0.125
r_symmetry_vdw_refined0.115
r_symmetry_hbond_refined0.109
r_nbtor_other0.079
r_chiral_restr0.054
r_mcbond_other0.03
r_bond_refined_d0.006
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5341
Nucleic Acid Atoms
Solvent Atoms41
Heterogen Atoms68

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
JDirectordata collection
HKL-2000data reduction
PHASERphasing