3UIX

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 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
3.2161.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.006α = 90
b = 97.006β = 90
c = 80.898γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252009-04-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL32B21.0SPring-8BL32B2

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
12.229.141000.0830.08333.822.82206234.61
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)
12.22.321000.4270.4270.4370.0911.822.73189

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 REPLACEMENTTHROUGHOUT3A992.229.1420930110299.990.16820.16640.2011RANDOM30.7977
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]
0.860.430.86-1.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.174
r_dihedral_angle_4_deg16.469
r_dihedral_angle_3_deg13.041
r_dihedral_angle_1_deg5.666
r_scangle_it3.917
r_scbond_it2.406
r_mcangle_it1.661
r_angle_refined_deg1.294
r_mcbond_it0.861
r_chiral_restr0.096
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.174
r_dihedral_angle_4_deg16.469
r_dihedral_angle_3_deg13.041
r_dihedral_angle_1_deg5.666
r_scangle_it3.917
r_scbond_it2.406
r_mcangle_it1.661
r_angle_refined_deg1.294
r_mcbond_it0.861
r_chiral_restr0.096
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2168
Nucleic Acid Atoms
Solvent Atoms241
Heterogen Atoms36

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction