3UMW

Crystal structure of Pim1 kinase in complex with inhibitor (Z)-2-[(1H-indazol-3-yl)methylene]-6-methoxy-7-(piperazin-1-ylmethyl)benzofuran-3(2H)-one


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3A99 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5293100mM Citrate buffer pH 5.5, 200mM NaCl, 1M NH4HPO4, vapor diffusion, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.2962.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.28α = 90
b = 98.28β = 90
c = 80.641γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252011-01-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B21.0SPring-8BL26B2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.0832.17499.70.0780.07866.4266022660229.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.082.191000.3910.3910.4250.16626.43888

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 REPLACEMENTTHROUGHOUT3A992.0832.1726602134699.770.17490.17350.2003RANDOM30.2034
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]
0.630.320.63-0.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.036
r_dihedral_angle_4_deg16.623
r_dihedral_angle_3_deg13.182
r_dihedral_angle_1_deg5.5
r_scangle_it3.679
r_scbond_it2.226
r_mcangle_it1.591
r_angle_refined_deg1.506
r_mcbond_it0.828
r_chiral_restr0.089
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.036
r_dihedral_angle_4_deg16.623
r_dihedral_angle_3_deg13.182
r_dihedral_angle_1_deg5.5
r_scangle_it3.679
r_scbond_it2.226
r_mcangle_it1.591
r_angle_refined_deg1.506
r_mcbond_it0.828
r_chiral_restr0.089
r_bond_refined_d0.013
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2131
Nucleic Acid Atoms
Solvent Atoms237
Heterogen Atoms40

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
MOSFLMdata reduction