3H9F

Crystal Structure of Human Dual Specificity Protein Kinase (TTK) in complex with a pyrimido-diazepin ligand


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP627725% PEG3350, 0.2M MgCl2, 0.1M BT pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.160.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.69α = 90
b = 110.75β = 90
c = 115.2γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-04-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9782DiamondI02

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
12.641.41499.70.0610.06114.43.9142441420180.9
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)
12.62.741000.7330.417242042

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 REPLACEMENTTHROUGHOUT3CEK2.641142671419970999.520.210.210.2070.253RANDOM35.521
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]
-2.512.320.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.31
r_dihedral_angle_4_deg25.664
r_dihedral_angle_3_deg16.589
r_scangle_it12.84
r_scbond_it10.141
r_mcangle_it6.104
r_dihedral_angle_1_deg5.681
r_mcbond_it3.752
r_angle_refined_deg1.471
r_angle_other_deg1.359
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.31
r_dihedral_angle_4_deg25.664
r_dihedral_angle_3_deg16.589
r_scangle_it12.84
r_scbond_it10.141
r_mcangle_it6.104
r_dihedral_angle_1_deg5.681
r_mcbond_it3.752
r_angle_refined_deg1.471
r_angle_other_deg1.359
r_mcbond_other0.919
r_chiral_restr0.079
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2084
Nucleic Acid Atoms
Solvent Atoms11
Heterogen Atoms36

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction