4TY1

Crystal structure of human Pim-1 kinase in complex with an aminooxadiazole-indole inhibitor.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82771.0M LiCl, 0.1M TRIS pH8.0, 20% PEG6K
Crystal Properties
Matthews coefficientSolvent content
3.1961.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.081α = 90
b = 95.081β = 90
c = 80.842γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 922013-11-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5418

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
12.729.0499.70.0759.62.611535
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)
12.72.899.80.4572.282.6

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 REPLACEMENTTHROUGHOUT2.729.041091554999.650.18350.1810.2375RANDOM49.747
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]
0.230.230.23-0.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.256
r_dihedral_angle_3_deg16.021
r_dihedral_angle_4_deg14.019
r_long_range_B_refined6.757
r_long_range_B_other6.749
r_dihedral_angle_1_deg6.018
r_mcangle_it4.614
r_mcangle_other4.612
r_scangle_other4.212
r_mcbond_other2.836
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.256
r_dihedral_angle_3_deg16.021
r_dihedral_angle_4_deg14.019
r_long_range_B_refined6.757
r_long_range_B_other6.749
r_dihedral_angle_1_deg6.018
r_mcangle_it4.614
r_mcangle_other4.612
r_scangle_other4.212
r_mcbond_other2.836
r_mcbond_it2.835
r_scbond_it2.573
r_scbond_other2.572
r_angle_refined_deg1.409
r_angle_other_deg0.782
r_chiral_restr0.078
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2225
Nucleic Acid Atoms
Solvent Atoms40
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing