3GFW

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.627740% PEG300, 0.25M NaCl, 0.1M Na/K phosphate pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.1360.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.969α = 90
b = 114.686β = 90
c = 111.174γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-05-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.97642SLSX10SA

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
12.7460.30299.10.0730.07310.33.71219512085
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)
12.742.8999.90.6470.64723.71742

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 REPLACEMENTTHROUGHOUT3CEK2.7441.4122731208359898.450.2060.2060.2040.239RANDOM46.505
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]
-5.416.89-1.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.594
r_dihedral_angle_4_deg26.734
r_dihedral_angle_3_deg18.049
r_dihedral_angle_1_deg6.74
r_scangle_it2.446
r_angle_refined_deg1.58
r_scbond_it1.472
r_angle_other_deg0.92
r_mcangle_it0.897
r_mcbond_it0.467
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.594
r_dihedral_angle_4_deg26.734
r_dihedral_angle_3_deg18.049
r_dihedral_angle_1_deg6.74
r_scangle_it2.446
r_angle_refined_deg1.58
r_scbond_it1.472
r_angle_other_deg0.92
r_mcangle_it0.897
r_mcbond_it0.467
r_chiral_restr0.084
r_mcbond_other0.084
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1987
Nucleic Acid Atoms
Solvent Atoms5
Heterogen Atoms67

Software

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