4GW8

Human proto-oncogene serine threonine kinase (PIM1) in complex with a consensus peptide and Leucettine L41


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52770.16M Na(OAc), 0.08M BTProp pH 8.5 , 16% PEG3350, 8% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
359.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.006α = 90
b = 98.006β = 90
c = 80.497γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2008-10-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5418

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
1219.582970.0740.07417.76.3297552886234.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.1194.90.910.910.96.24114

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 2C3I219.582970828852145697.120.17760.17760.17580.213RANDOM36.226
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]
0.980.490.98-1.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.563
r_dihedral_angle_4_deg15.592
r_dihedral_angle_3_deg14.219
r_scangle_it9.303
r_scbond_it7.728
r_dihedral_angle_1_deg5.918
r_mcangle_it4.531
r_mcbond_it3.392
r_angle_refined_deg1.515
r_mcbond_other1.145
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.563
r_dihedral_angle_4_deg15.592
r_dihedral_angle_3_deg14.219
r_scangle_it9.303
r_scbond_it7.728
r_dihedral_angle_1_deg5.918
r_mcangle_it4.531
r_mcbond_it3.392
r_angle_refined_deg1.515
r_mcbond_other1.145
r_angle_other_deg0.935
r_chiral_restr0.098
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2284
Nucleic Acid Atoms
Solvent Atoms198
Heterogen Atoms27

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
MOSFLMdata reduction