3CXW

Crystal structure of human proto-oncogene serine threonine kinase (PIM1) in complex with a consensus peptide and a beta carboline ligand I


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2C3IPDB entry 2C3I

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.14 M Sodium malonate, 0.07 M Bis-Tris-Propane pH 7.5, 14 % PEG 3350, 7 % Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.0459.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.371α = 90
b = 98.371β = 90
c = 81.332γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.97912SLSX10SA

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
12.1501000.1260.1266.33.82620326203
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)
12.12.181000.7243.82592

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2C3I2.136.712616826168133099.950.1660.1660.1640.206RANDOM19.425
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]
0.120.060.12-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.886
r_dihedral_angle_4_deg17.488
r_dihedral_angle_3_deg14.065
r_scangle_it7.364
r_dihedral_angle_1_deg6.494
r_scbond_it5.51
r_mcangle_it3.4
r_mcbond_it2.196
r_angle_other_deg1.653
r_angle_refined_deg1.477
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.886
r_dihedral_angle_4_deg17.488
r_dihedral_angle_3_deg14.065
r_scangle_it7.364
r_dihedral_angle_1_deg6.494
r_scbond_it5.51
r_mcangle_it3.4
r_mcbond_it2.196
r_angle_other_deg1.653
r_angle_refined_deg1.477
r_mcbond_other0.638
r_chiral_restr0.089
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2263
Nucleic Acid Atoms
Solvent Atoms217
Heterogen Atoms26

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-2000data reduction