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Crystal structure of DCLK1 kinase domain in complex with ruxolitinib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JZJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 296 25% (w/v) polyethylene glycol (PEG) 3,350, 0.1 M Bis-Tris (pH 6.5), and 200 mM magne-sium chloride
Crystal Properties Matthews coefficient Solvent content 2.27 45.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.248 α = 90 b = 80.118 β = 90.662 c = 59.338 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 CCD BRUKER SMART 6500 2020-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 1.0000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 2.09 50 95.5 0.05 0.067 0.998 8.41 2 31156
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.21 90.8 0.725 0.833 0.662 1.92
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5JZJ 2.1 47.727 31156 1568 99.283 0.213 0.2104 0.217 0.2533 0.2527 62.345
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] 1.299 -5.598 -5.637 4.467
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.211 r_dihedral_angle_4_deg 16.144 r_dihedral_angle_3_deg 13.126 r_lrange_it 7.042 r_lrange_other 7.042 r_dihedral_angle_1_deg 6.387 r_mcangle_it 4.772 r_mcangle_other 4.771 r_scangle_it 4.52 r_scangle_other 4.519
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.211 r_dihedral_angle_4_deg 16.144 r_dihedral_angle_3_deg 13.126 r_lrange_it 7.042 r_lrange_other 7.042 r_dihedral_angle_1_deg 6.387 r_mcangle_it 4.772 r_mcangle_other 4.771 r_scangle_it 4.52 r_scangle_other 4.519 r_mcbond_it 2.882 r_mcbond_other 2.881 r_scbond_it 2.808 r_scbond_other 2.806 r_angle_refined_deg 1.138 r_angle_other_deg 1.089 r_symmetry_nbd_other 0.184 r_nbd_other 0.183 r_nbd_refined 0.179 r_symmetry_xyhbond_nbd_refined 0.168 r_nbtor_refined 0.152 r_xyhbond_nbd_refined 0.12 r_symmetry_nbd_refined 0.076 r_symmetry_nbtor_other 0.071 r_chiral_restr 0.04 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4236 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing