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The co-crystal structure of DYRK2 with AF-4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7EJV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289.15 0.05M HEPES pH7.0
15% PEG3350
1% Trptone
1mM NaN3
Crystal Properties Matthews coefficient Solvent content 3.14 60.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.85 α = 90 b = 60.55 β = 113.11 c = 155.28 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 289.15 PIXEL DECTRIS PILATUS 6M 2023-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.979 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.87 58.48 99.73 0.122 0.996 9.9 6.7 25668
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.87 2.94 99.83 1.017 0.871
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 NONE 2.87 58.48 1.36 25654 1998 99.73 0.2478 0.2441 0.2443 0.292 0.2921
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 12.656 f_angle_d 0.429 f_chiral_restr 0.038 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6262 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 60
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction XDS data scaling PHASER phasing