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Crystal structure of di-phosphorylated human CLK1 in complex with 5-(6,7-dichloro-1H-indol-3-yl)pyrimidin-4-amine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6R8J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 24% PEG3350, 200mM MgCl2, 100mM BisTris (pH 6.5)
Crystal Properties Matthews coefficient Solvent content 2.45 49.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.22 α = 90 b = 68.22 β = 90 c = 283.14 γ = 120
Symmetry Space Group P 65 2 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 PILATUS3 6M 2016-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.976 ESRF ID23-1
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 1.81 100 99.7 0.066 20.68 5.73 36760
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.81 1.87 99.8 1.17 0.679
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 6R8J 1.81 50.128 36755 1837 99.704 0.195 0.1926 0.2027 0.2423 0.2501 38.601
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] 0.911 0.455 0.911 -2.955
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.034 r_dihedral_angle_4_deg 19.422 r_dihedral_angle_3_deg 15.132 r_lrange_it 8.635 r_lrange_other 8.619 r_scangle_it 7.348 r_scangle_other 7.346 r_dihedral_angle_1_deg 7.152 r_scbond_it 5.168 r_scbond_other 5.166
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.034 r_dihedral_angle_4_deg 19.422 r_dihedral_angle_3_deg 15.132 r_lrange_it 8.635 r_lrange_other 8.619 r_scangle_it 7.348 r_scangle_other 7.346 r_dihedral_angle_1_deg 7.152 r_scbond_it 5.168 r_scbond_other 5.166 r_mcangle_other 4.857 r_mcangle_it 4.856 r_mcbond_it 3.882 r_mcbond_other 3.878 r_angle_refined_deg 1.849 r_angle_other_deg 1.44 r_nbd_other 0.229 r_nbd_refined 0.223 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.176 r_symmetry_xyhbond_nbd_refined 0.174 r_xyhbond_nbd_refined 0.166 r_symmetry_nbd_refined 0.098 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.082 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2719 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction XSCALE data scaling MOLREP phasing