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Structure of DYRK1A in complex with compound 53
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, SITTING DROP 5.5 293 15% PEG 4K, 0.2M ammonium sulphate, 0.1M sodium DL-malate buffer pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.4 48.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.25 α = 90 b = 85.05 β = 107.94 c = 84.74 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 PILATUS 6M 2011-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9793 ESRF ID29
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 2.02 58.5 99.1 0.058 11.8 3.3 51134
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 2.02 2.09 99.8 0.676 1.8 3.5
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 2.1 25 43210 2276 98.82 0.1984 0.1966 0.2058 0.2308 0.2381 RANDOM 39.554
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] 1.59 -0.93 -2.18 0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.815 r_dihedral_angle_4_deg 22.48 r_dihedral_angle_3_deg 15.554 r_dihedral_angle_1_deg 6.119 r_angle_refined_deg 1.545 r_angle_other_deg 1.293 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.815 r_dihedral_angle_4_deg 22.48 r_dihedral_angle_3_deg 15.554 r_dihedral_angle_1_deg 6.119 r_angle_refined_deg 1.545 r_angle_other_deg 1.293 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5405 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 63
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction