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Crystal structure of DYRK1A in complex with Curcumin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EIS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.1 M Bis-Tris pH 5.8, 26 % w/v PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 2.67 53.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.048 α = 90 b = 132.048 β = 90 c = 91.787 γ = 120
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 EIGER2 X 16M 2021-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.69 48.53 97.1 0.139 0.158 0.073 0.989 9 4.1 24625 55.39
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.69 2.82 98.2 1.364 1.593 0.798 0.44 3.4
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 2.69 48.53 1.34 23391 1143 92.09 0.2423 0.2403 0.2435 0.2782 0.28 73.28
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 17.5814 f_angle_d 0.8181 f_chiral_restr 0.043 f_plane_restr 0.0088 f_bond_d 0.0056
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5096 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 67
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing