3K2L

Crystal Structure of dual-specificity tyrosine phosphorylation regulated kinase 2 (DYRK2)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VX3PDB ENTRY 2VX3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52771.26M (NH4)2SO4, 0.20M Li2SO4, 0.1M TRIS pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.6553.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.285α = 90
b = 84.285β = 90
c = 148.505γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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
12.3642.1999.80.0820.08212.26.2228472280163.6
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)
12.362.491000.8990.8992.16.43275

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 2VX32.3640.542275822694116099.720.2280.2280.2250.288RANDOM35.014
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]
1.531.53-3.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.874
r_dihedral_angle_4_deg20.908
r_dihedral_angle_3_deg16.034
r_scangle_it12.453
r_scbond_it10.724
r_dihedral_angle_1_deg6.918
r_mcangle_it6.116
r_mcbond_it4.196
r_angle_refined_deg1.602
r_mcbond_other1.248
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.874
r_dihedral_angle_4_deg20.908
r_dihedral_angle_3_deg16.034
r_scangle_it12.453
r_scbond_it10.724
r_dihedral_angle_1_deg6.918
r_mcangle_it6.116
r_mcbond_it4.196
r_angle_refined_deg1.602
r_mcbond_other1.248
r_angle_other_deg0.915
r_chiral_restr0.092
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3143
Nucleic Acid Atoms
Solvent Atoms58
Heterogen Atoms13

Software

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