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Crystal structure of human CLK1 kinase in complex with compound 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z57
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.8 301 0.10 M Li2-Sulfate, 0.10 M Tris/HCl, pH 8.8, 15.00 %(w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.64 53.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.752 α = 90 b = 64.358 β = 119.43 c = 80.822 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 101 PIXEL DECTRIS PILATUS3 2M 2015-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.966 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.8 29.35 97.9 0.11 10.3 2.7 37677
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 97.4 0.62 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.8 29.35 35813 1864 97.78 0.18015 0.17709 0.1917 0.24034 0.2468 RANDOM 28.899
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] 0.54 -0.44 1.12 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.429 r_dihedral_angle_4_deg 17.201 r_dihedral_angle_3_deg 14.404 r_long_range_B_refined 9.869 r_long_range_B_other 8.87 r_dihedral_angle_1_deg 5.957 r_scangle_other 5.359 r_mcangle_it 3.867 r_mcangle_other 3.867 r_scbond_it 3.536
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.429 r_dihedral_angle_4_deg 17.201 r_dihedral_angle_3_deg 14.404 r_long_range_B_refined 9.869 r_long_range_B_other 8.87 r_dihedral_angle_1_deg 5.957 r_scangle_other 5.359 r_mcangle_it 3.867 r_mcangle_other 3.867 r_scbond_it 3.536 r_scbond_other 3.535 r_mcbond_it 2.674 r_mcbond_other 2.673 r_angle_refined_deg 1.435 r_angle_other_deg 0.963 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2762 Nucleic Acid Atoms Solvent Atoms 668 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing