6EIF

DYRK1A in complex with XMD7-117


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1 M KSCN; 0.1M NaCl; 14% PEG 3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6553.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.44α = 90
b = 88.536β = 90
c = 231.142γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-05-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.976251ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
12.225099.10.1498.64.989260
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.932.2296.20.7750.7431.9313806

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 REPLACEMENTTHROUGHOUT4nct2.2248.5784728452999.120.219980.218360.25049RANDOM46.94
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]
-14.635.379.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.773
r_dihedral_angle_4_deg14.262
r_dihedral_angle_3_deg12.647
r_dihedral_angle_1_deg5.029
r_long_range_B_refined2.869
r_long_range_B_other2.832
r_angle_refined_deg1.076
r_mcangle_it1.013
r_mcangle_other1.013
r_angle_other_deg0.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.773
r_dihedral_angle_4_deg14.262
r_dihedral_angle_3_deg12.647
r_dihedral_angle_1_deg5.029
r_long_range_B_refined2.869
r_long_range_B_other2.832
r_angle_refined_deg1.076
r_mcangle_it1.013
r_mcangle_other1.013
r_angle_other_deg0.86
r_scangle_other0.632
r_mcbond_it0.557
r_mcbond_other0.557
r_scbond_it0.346
r_scbond_other0.346
r_chiral_restr0.059
r_bond_refined_d0.007
r_gen_planes_refined0.004
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 Atoms10771
Nucleic Acid Atoms
Solvent Atoms234
Heterogen Atoms100

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing