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Structure of DYRK1A in complex with compound 46
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 6.5 293 12% PEG3350, 0.1M MES buffer pH 6.5, 0.2M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.5 50.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.959 α = 90 b = 81.959 β = 90 c = 123.892 γ = 90
Symmetry Space Group P 43 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 PIXEL DECTRIS PILATUS 6M 2011-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 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 2.69 50 98.1 0.197 7.6 3.9 21996
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 2.69 2.85 94.3 1.715 0.9 3.7
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 2vx3 2.8 25 10252 517 98.42 0.1824 0.1797 0.1869 0.237 0.232 RANDOM 52.686
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] 2.99 2.99 -5.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.779 r_dihedral_angle_4_deg 21.469 r_dihedral_angle_3_deg 16.438 r_dihedral_angle_1_deg 6.33 r_angle_refined_deg 1.495 r_angle_other_deg 1.23 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.779 r_dihedral_angle_4_deg 21.469 r_dihedral_angle_3_deg 16.438 r_dihedral_angle_1_deg 6.33 r_angle_refined_deg 1.495 r_angle_other_deg 1.23 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2656 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms 29
Software Software Software Name Purpose XDS data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction