5O12

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 DROP8293Tris, potassium sodium tartrate tetrahydrate
Crystal Properties
Matthews coefficientSolvent content
3.5765.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.672α = 90
b = 97.672β = 90
c = 80.579γ = 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
12.442.2910014.75.217210

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 REPLACEMENTTHROUGHOUT4ALW2.442.291636282299.980.178930.176830.22273RANDOM52.909
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]
0.70.350.7-2.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.036
r_dihedral_angle_4_deg18.678
r_dihedral_angle_3_deg15.007
r_dihedral_angle_1_deg6.742
r_long_range_B_refined6.436
r_long_range_B_other6.435
r_scangle_other5.265
r_mcangle_it3.972
r_mcangle_other3.969
r_scbond_it3.709
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.036
r_dihedral_angle_4_deg18.678
r_dihedral_angle_3_deg15.007
r_dihedral_angle_1_deg6.742
r_long_range_B_refined6.436
r_long_range_B_other6.435
r_scangle_other5.265
r_mcangle_it3.972
r_mcangle_other3.969
r_scbond_it3.709
r_scbond_other3.709
r_mcbond_it2.836
r_mcbond_other2.835
r_angle_refined_deg1.993
r_angle_other_deg0.904
r_chiral_restr0.105
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_gen_planes_other0.003
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 Atoms2130
Nucleic Acid Atoms
Solvent Atoms53
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing