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Crystal Structure of dual-specificity tyrosine phosphorylation regulated kinase 2 (DYRK2) in complex with an indirubin ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K2L PDB ENTRY 3K2L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.2M Na(Acetate), 0.1M cacodylate pH 6.5, 30% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.67 53.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.28 α = 90 b = 84.28 β = 90 c = 149.12 γ = 90
Symmetry Space Group P 42 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 CCD ADSC QUANTUM 315r 2009-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9802 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.28 46.552 100 0.105 0.105 12.2 7.4 25294 25294 48.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.28 2.4 100 0.885 0.885 2.5 7.6 3617
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 3K2L 2.28 42.81 25362 25247 1292 99.94 0.211 0.211 0.209 0.2111 0.26 0.2616 RANDOM 22.469
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] 0.34 0.34 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.292 r_dihedral_angle_4_deg 21.525 r_dihedral_angle_3_deg 16.523 r_scangle_it 10.267 r_dihedral_angle_1_deg 8.519 r_scbond_it 8.396 r_mcangle_it 5.217 r_mcbond_it 3.633 r_angle_refined_deg 1.548 r_mcbond_other 1.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.292 r_dihedral_angle_4_deg 21.525 r_dihedral_angle_3_deg 16.523 r_scangle_it 10.267 r_dihedral_angle_1_deg 8.519 r_scbond_it 8.396 r_mcangle_it 5.217 r_mcbond_it 3.633 r_angle_refined_deg 1.548 r_mcbond_other 1.146 r_angle_other_deg 0.939 r_chiral_restr 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_gen_planes_other 0.007 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3188 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 29
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction GDA data collection MOSFLM data reduction