3E88

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
2.2144.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.885α = 90
b = 116.885β = 90
c = 45.115γ = 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
12.541.211000.1794.15.7238012
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)
12.52.591000.675.7

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 REPLACEMENTTHROUGHOUT2.541.2122560121999.890.232030.229760.273RANDOM26.795
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]
0.040.020.04-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.952
r_dihedral_angle_3_deg13.591
r_dihedral_angle_4_deg13.151
r_dihedral_angle_1_deg5.181
r_angle_refined_deg1.17
r_angle_other_deg0.764
r_scangle_it0.601
r_mcangle_it0.555
r_mcbond_it0.521
r_scbond_it0.391
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.952
r_dihedral_angle_3_deg13.591
r_dihedral_angle_4_deg13.151
r_dihedral_angle_1_deg5.181
r_angle_refined_deg1.17
r_angle_other_deg0.764
r_scangle_it0.601
r_mcangle_it0.555
r_mcbond_it0.521
r_scbond_it0.391
r_symmetry_vdw_other0.204
r_nbd_refined0.18
r_nbtor_refined0.176
r_nbd_other0.172
r_symmetry_vdw_refined0.12
r_xyhbond_nbd_refined0.113
r_nbtor_other0.079
r_mcbond_other0.073
r_chiral_restr0.052
r_symmetry_hbond_refined0.043
r_bond_refined_d0.005
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 Atoms5426
Nucleic Acid Atoms
Solvent Atoms62
Heterogen Atoms68

Software

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