5O13

Crystal structure of PIM1 kinase in complex with small-molecule inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4ALW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293Tris, potassium sodium tartrate tetrahydrate
Crystal Properties
Matthews coefficientSolvent content
3.564.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.735α = 90
b = 96.735β = 90
c = 81.765γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-06-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91841BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.4429.2699.638.55.116181

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 REPLACEMENTTHROUGHOUT4ALW2.4429.261531783499.520.161830.159140.21405RANDOM46.561
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]
0.880.440.88-2.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.186
r_dihedral_angle_4_deg16.303
r_dihedral_angle_3_deg14.92
r_long_range_B_refined7.789
r_long_range_B_other7.787
r_dihedral_angle_1_deg6.901
r_scangle_other5.83
r_mcangle_other4.142
r_mcangle_it4.14
r_scbond_it3.825
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.186
r_dihedral_angle_4_deg16.303
r_dihedral_angle_3_deg14.92
r_long_range_B_refined7.789
r_long_range_B_other7.787
r_dihedral_angle_1_deg6.901
r_scangle_other5.83
r_mcangle_other4.142
r_mcangle_it4.14
r_scbond_it3.825
r_scbond_other3.824
r_mcbond_it2.789
r_mcbond_other2.789
r_angle_refined_deg2.027
r_angle_other_deg0.874
r_chiral_restr0.107
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_gen_planes_other0.006
r_bond_other_d0.001
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 Atoms2161
Nucleic Acid Atoms
Solvent Atoms90
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing