5A54

DYRK1A IN COMPLEX WITH NITRO BENZOTHIAZOLE FRAGMENT


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4NCTPDB ENTRY 4NCT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.82930.1 M KSCN; 0.1M KCL; 14% PEG 3350, PH 6.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties
Matthews coefficientSolvent content
2.652.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.818α = 90
b = 88.015β = 90
c = 228.819γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-01-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

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
12.635099.70.114.226.5534932.27
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)
12.632.7998.80.82.276.6

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 4NCT2.6348.1951440205299.460.223570.222320.25461RANDOM59.49
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]
-0.6935.6-34.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.874
r_dihedral_angle_4_deg15.809
r_dihedral_angle_3_deg14.317
r_dihedral_angle_1_deg4.855
r_mcangle_it2.975
r_mcbond_it1.739
r_mcbond_other1.738
r_scbond_it1.325
r_angle_refined_deg0.974
r_angle_other_deg0.693
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.874
r_dihedral_angle_4_deg15.809
r_dihedral_angle_3_deg14.317
r_dihedral_angle_1_deg4.855
r_mcangle_it2.975
r_mcbond_it1.739
r_mcbond_other1.738
r_scbond_it1.325
r_angle_refined_deg0.974
r_angle_other_deg0.693
r_chiral_restr0.053
r_bond_refined_d0.006
r_gen_planes_refined0.003
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10955
Nucleic Acid Atoms
Solvent Atoms44
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing