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Crystal structure of human DYRK1A in complex with ARN25565
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7OY6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.4 293 15-20% PEG1000, 50 mM Mes 6.4, 100 mM KCl
Crystal Properties Matthews coefficient Solvent content 2.58 52.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.27 α = 90 b = 94.27 β = 90 c = 48.7 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2022-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.595 66.66 100 0.026 0.999 20.2 13.5 13488
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.595 2.64 0.397 0.804 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.7 66.66 1.35 11976 610 99.99 0.1957 0.1937 0.1923 0.2299 0.2192
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 9.355 f_angle_d 1.016 f_chiral_restr 0.059 f_bond_d 0.009 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2806 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 27
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling XDS data reduction PHASER phasing