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Human DYRK2 bound to Curcumin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AZF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2M sodium potassium phosphate, 20% PEG 3350 and 10% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.63 53.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.642 α = 90 b = 83.642 β = 90 c = 148.916 γ = 90
Symmetry Space Group P 42 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 2011-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.2 40.26 99.9 0.072 15 5.9 27566
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 99.8 0.836 2.3 5.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4AZF 2.2 40.3 26114 1411 99.77 0.19248 0.18974 0.1921 0.24263 0.2419 RANDOM 72.456
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] 1.11 1.11 -2.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.725 r_dihedral_angle_4_deg 19.742 r_dihedral_angle_3_deg 14.914 r_long_range_B_other 7.228 r_long_range_B_refined 7.22 r_dihedral_angle_1_deg 6.24 r_scangle_other 5.586 r_mcangle_it 4.456 r_mcangle_other 4.455 r_scbond_it 3.845
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.725 r_dihedral_angle_4_deg 19.742 r_dihedral_angle_3_deg 14.914 r_long_range_B_other 7.228 r_long_range_B_refined 7.22 r_dihedral_angle_1_deg 6.24 r_scangle_other 5.586 r_mcangle_it 4.456 r_mcangle_other 4.455 r_scbond_it 3.845 r_scbond_other 3.821 r_mcbond_it 3.225 r_mcbond_other 3.223 r_angle_refined_deg 1.272 r_angle_other_deg 0.827 r_chiral_restr 0.06 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 3219 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing