5O11

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
3.4163.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.052α = 90
b = 96.052β = 90
c = 80.297γ = 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
12.448.0399.211.96.916422

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 REPLACEMENTTHROUGHOUT4ALW2.448.031557285099.210.167140.164610.21159RANDOM43.251
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]
1.450.731.45-4.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.104
r_dihedral_angle_4_deg15.652
r_dihedral_angle_3_deg14.776
r_dihedral_angle_1_deg6.691
r_long_range_B_other6.214
r_long_range_B_refined6.211
r_scangle_other4.07
r_mcangle_other3.422
r_mcangle_it3.421
r_scbond_it2.768
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.104
r_dihedral_angle_4_deg15.652
r_dihedral_angle_3_deg14.776
r_dihedral_angle_1_deg6.691
r_long_range_B_other6.214
r_long_range_B_refined6.211
r_scangle_other4.07
r_mcangle_other3.422
r_mcangle_it3.421
r_scbond_it2.768
r_scbond_other2.748
r_mcbond_it2.228
r_mcbond_other2.228
r_angle_refined_deg1.76
r_angle_other_deg0.834
r_chiral_restr0.098
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_gen_planes_other0.004
r_bond_other_d0.002
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 Atoms2138
Nucleic Acid Atoms
Solvent Atoms97
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing