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Crystal structure of DYRK1A with harmine-derivatized AnnH-75 inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WO6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 277 31% PEG 400, 0.2 M lithium sulfate, 0.1 M Tris, pH 9.0
Crystal Properties Matthews coefficient Solvent content 3.26 62.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 265.567 α = 90 b = 65.444 β = 114.44 c = 138.648 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 100 PIXEL DECTRIS PILATUS 2M 2013-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92000 Diamond I04-1
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 2.9 48.34 99.5 0.126 10.6 6.7 48349 58.2
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 2.9 3.06 99.5 0.928 2 6.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2WO6 2.9 48.34 45905 2443 99.34 0.24478 0.24302 0.27715 0.2581 RANDOM 75.108
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] 0.28 -2.92 -2.02 3.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.768 r_dihedral_angle_4_deg 19.991 r_dihedral_angle_3_deg 15.426 r_long_range_B_refined 7.575 r_long_range_B_other 7.574 r_dihedral_angle_1_deg 6.708 r_scangle_other 3.658 r_mcangle_it 3.401 r_mcangle_other 3.4 r_scbond_it 2.453
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.768 r_dihedral_angle_4_deg 19.991 r_dihedral_angle_3_deg 15.426 r_long_range_B_refined 7.575 r_long_range_B_other 7.574 r_dihedral_angle_1_deg 6.708 r_scangle_other 3.658 r_mcangle_it 3.401 r_mcangle_other 3.4 r_scbond_it 2.453 r_scbond_other 2.399 r_mcbond_it 1.984 r_mcbond_other 1.984 r_angle_refined_deg 1.223 r_angle_other_deg 0.825 r_chiral_restr 0.063 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.005 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 11253 Nucleic Acid Atoms Solvent Atoms 306 Heterogen Atoms 135
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing