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Structure of DYRK1A in complex with compound 34
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VX3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 0.1M Hepes buffer at pH 7.5, 20% Peg4k, 0.2M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.38 48.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.361 α = 90 b = 85.368 β = 107.06 c = 84.804 γ = 90
Symmetry Space Group P 1 21 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 EIGER2 XE 16M 2019-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 2.27 58.8 61.5 0.113 8.2 3.1 22364
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 2.27 2.38 0.691 1.6
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 2vx3 2.3 25 21041 1058 63.38 0.2219 0.2187 0.2851 0.284 RANDOM 40.683
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] 0.16 -0.2 -0.49 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.109 r_dihedral_angle_4_deg 22.494 r_dihedral_angle_3_deg 21.156 r_dihedral_angle_1_deg 5.654 r_angle_refined_deg 1.513 r_angle_other_deg 1.215 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.109 r_dihedral_angle_4_deg 22.494 r_dihedral_angle_3_deg 21.156 r_dihedral_angle_1_deg 5.654 r_angle_refined_deg 1.513 r_angle_other_deg 1.215 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5350 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 57
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction