4YLK

Crystal structure of DYRK1A in complex with 10-Chloro-substituted 11H-indolo[3,2-c]quinolone-6-carboxylic acid inhibitor 5s


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WO6PDB entry 2WO6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.62772 M ammonium sulfate, 0.1 M citrate, pH 5.6, 0.2 M potassium/sodium tartrate
Crystal Properties
Matthews coefficientSolvent content
2.4950.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.97α = 90
b = 69.87β = 117.69
c = 67.86γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2012-07-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92000DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.430.2897.10.07710.74.47884210.6
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)
11.41.4897.30.3863.54.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2WO61.430.0774899394296.970.155970.154850.17671RANDOM15.023
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]
-0.27-0.510.240.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.991
r_dihedral_angle_4_deg23.43
r_dihedral_angle_3_deg11.454
r_dihedral_angle_1_deg6.068
r_long_range_B_refined5.712
r_long_range_B_other5.711
r_angle_refined_deg1.775
r_scangle_other1.398
r_mcangle_it0.923
r_mcangle_other0.922
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.991
r_dihedral_angle_4_deg23.43
r_dihedral_angle_3_deg11.454
r_dihedral_angle_1_deg6.068
r_long_range_B_refined5.712
r_long_range_B_other5.711
r_angle_refined_deg1.775
r_scangle_other1.398
r_mcangle_it0.923
r_mcangle_other0.922
r_scbond_it0.916
r_scbond_other0.915
r_angle_other_deg0.775
r_mcbond_it0.545
r_mcbond_other0.544
r_chiral_restr0.1
r_bond_refined_d0.016
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2786
Nucleic Acid Atoms
Solvent Atoms557
Heterogen Atoms101

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing