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Crystal structure of DYRK1A in complex with RD0448
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ANR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 100mM BIS-TRIS propane, 200 mM Sodium fluoride, 22% PEG3350, pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.72 54.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.088 α = 90 b = 87.577 β = 90 c = 227.146 γ = 90
Symmetry Space Group P 21 21 21
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 2017-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.68 47.85 100 0.131 10.3 6.6 49716
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.68 2.77 0.963
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 3ANR 2.68 45 47210 2434 99.94 0.19143 0.18843 0.1899 0.24938 0.2457 RANDOM 61.619
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] -0.27 1.33 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.863 r_dihedral_angle_4_deg 17.44 r_dihedral_angle_3_deg 14.37 r_long_range_B_refined 5.502 r_long_range_B_other 5.499 r_dihedral_angle_1_deg 4.972 r_mcangle_other 3.727 r_mcangle_it 3.726 r_scangle_other 3.502 r_mcbond_it 2.482
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.863 r_dihedral_angle_4_deg 17.44 r_dihedral_angle_3_deg 14.37 r_long_range_B_refined 5.502 r_long_range_B_other 5.499 r_dihedral_angle_1_deg 4.972 r_mcangle_other 3.727 r_mcangle_it 3.726 r_scangle_other 3.502 r_mcbond_it 2.482 r_mcbond_other 2.481 r_scbond_it 2.412 r_scbond_other 2.412 r_angle_refined_deg 1.156 r_angle_other_deg 1.057 r_rigid_bond_restr 0.395 r_chiral_restr 0.038 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11120 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing