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Crystal Structure of dual-specificity tyrosine phosphorylation regulated kinase 2 (DYRK2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VX3 PDB ENTRY 2VX3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 1.26M (NH4)2SO4, 0.20M Li2SO4, 0.1M TRIS pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.65 53.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.285 α = 90 b = 84.285 β = 90 c = 148.505 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 2009-06-29 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) 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 2.36 42.19 99.8 0.082 0.082 12.2 6.2 22847 22801 63.6
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 2.36 2.49 100 0.899 0.899 2.1 6.4 3275
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 2VX3 2.36 40.54 22758 22694 1160 99.72 0.228 0.228 0.225 0.2217 0.288 0.2805 RANDOM 35.014
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] 1.53 1.53 -3.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.874 r_dihedral_angle_4_deg 20.908 r_dihedral_angle_3_deg 16.034 r_scangle_it 12.453 r_scbond_it 10.724 r_dihedral_angle_1_deg 6.918 r_mcangle_it 6.116 r_mcbond_it 4.196 r_angle_refined_deg 1.602 r_mcbond_other 1.248
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.874 r_dihedral_angle_4_deg 20.908 r_dihedral_angle_3_deg 16.034 r_scangle_it 12.453 r_scbond_it 10.724 r_dihedral_angle_1_deg 6.918 r_mcangle_it 6.116 r_mcbond_it 4.196 r_angle_refined_deg 1.602 r_mcbond_other 1.248 r_angle_other_deg 0.915 r_chiral_restr 0.092 r_bond_refined_d 0.014 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 3143 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 13
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection MOSFLM data reduction