2XJ1

Protein kinase Pim-1 in complex with small molecule inibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherIN-HOUSE PIM-1 STRUCTURE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.50.9 M (NH4)2HPO4,0.1 M SODIUM CITRATE PH=5.5 , 0.2M NACL
Crystal Properties
Matthews coefficientSolvent content
3.2862.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.75α = 90
b = 95.75β = 90
c = 80.932γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2008-06-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.2BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.1348.694.80.0635.4922397
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.132.2163.10.323.14.4

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 REPLACEMENTTHROUGHOUTIN-HOUSE PIM-1 STRUCTURE2.1348.6221246112394.80.17790.176090.21151RANDOM52.464
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]
-0.26-0.13-0.260.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.624
r_dihedral_angle_4_deg15.684
r_dihedral_angle_3_deg15.154
r_scangle_it6.479
r_dihedral_angle_1_deg5.512
r_scbond_it4.815
r_mcangle_it3.074
r_mcbond_it2.095
r_angle_refined_deg1.246
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.624
r_dihedral_angle_4_deg15.684
r_dihedral_angle_3_deg15.154
r_scangle_it6.479
r_dihedral_angle_1_deg5.512
r_scbond_it4.815
r_mcangle_it3.074
r_mcbond_it2.095
r_angle_refined_deg1.246
r_nbtor_refined0.305
r_nbd_refined0.192
r_symmetry_vdw_refined0.163
r_xyhbond_nbd_refined0.119
r_symmetry_hbond_refined0.107
r_chiral_restr0.083
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2234
Nucleic Acid Atoms
Solvent Atoms108
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing