☰ Navigation Tabs
Structure of DYRK2 in complex with compound 58
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K2L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 25% PEG 4k, 0.1M Tris buffer pH 8.5, 0.1M Li sulphate
Crystal Properties Matthews coefficient Solvent content 2.68 54.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.24 α = 90 b = 84.24 β = 90 c = 150.06 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 PIXEL DECTRIS PILATUS 6M 2010-01-30 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 2.81 84.2 100 0.097 12.2 6.9 13805
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 2.81 2.88 99.9 0.874 2.2 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 3k2l 2.85 20 12548 655 99.55 0.1879 0.1851 0.1879 0.2448 0.2433 RANDOM 69.943
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] 2.26 2.26 -4.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.481 r_dihedral_angle_4_deg 25.309 r_dihedral_angle_3_deg 21.301 r_dihedral_angle_1_deg 5.632 r_angle_refined_deg 1.591 r_angle_other_deg 1.274 r_chiral_restr 0.064 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.481 r_dihedral_angle_4_deg 25.309 r_dihedral_angle_3_deg 21.301 r_dihedral_angle_1_deg 5.632 r_angle_refined_deg 1.591 r_angle_other_deg 1.274 r_chiral_restr 0.064 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3185 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 30
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction