4YLL

Crystal structure of DYRK1AA in complex with 10-Bromo-substituted 11H-indolo[3,2-c]quinolone-6-carboxylic acid inhibitor 5t


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
2.550.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.03α = 90
b = 69.86β = 117.72
c = 67.9γ = 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
11.428.21950.05912.43.37708310.8
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)
11.41.4895.40.2684.43.3

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 2WO61.427.4273218385994.690.151610.150530.17163RANDOM14.565
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]
-0.07-0.350.060.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.013
r_dihedral_angle_4_deg21.442
r_dihedral_angle_3_deg10.942
r_dihedral_angle_1_deg6.008
r_long_range_B_refined5.277
r_long_range_B_other5.276
r_sphericity_bonded2.698
r_angle_refined_deg1.667
r_scangle_other1.305
r_scbond_it0.866
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.013
r_dihedral_angle_4_deg21.442
r_dihedral_angle_3_deg10.942
r_dihedral_angle_1_deg6.008
r_long_range_B_refined5.277
r_long_range_B_other5.276
r_sphericity_bonded2.698
r_angle_refined_deg1.667
r_scangle_other1.305
r_scbond_it0.866
r_scbond_other0.865
r_mcangle_other0.854
r_mcangle_it0.853
r_angle_other_deg0.771
r_mcbond_it0.507
r_mcbond_other0.501
r_chiral_restr0.094
r_bond_refined_d0.015
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2783
Nucleic Acid Atoms
Solvent Atoms577
Heterogen Atoms83

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing