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Crystal structure of CLK1 in complexed with furo[3,2-b]pyridine compound VN316 (derivative of compound 12h)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6G33
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 24-28% 1,2-propanediol, 5% glycerol, 0.1M sodium/potassium phosphate
Crystal Properties Matthews coefficient Solvent content 2.58 52.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.129 α = 90 b = 117.55 β = 99.1 c = 92.27 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 PIXEL DECTRIS PILATUS3 2M 2016-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
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 2.55 91.11 97.3 0.136 8.8 5.4 38161
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 2.55 2.69 94.3 0.757 2 4.9
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 6G33 2.55 91.11 36172 1967 97.1 0.19491 0.19345 0.1977 0.22146 0.2261 RANDOM 51.62
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] 1.29 -0.64 -1.23 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.984 r_dihedral_angle_4_deg 17.808 r_dihedral_angle_3_deg 14.568 r_dihedral_angle_1_deg 6.323 r_long_range_B_refined 4.922 r_long_range_B_other 4.922 r_scangle_other 2.249 r_mcangle_it 2.042 r_mcangle_other 2.042 r_angle_refined_deg 1.394
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.984 r_dihedral_angle_4_deg 17.808 r_dihedral_angle_3_deg 14.568 r_dihedral_angle_1_deg 6.323 r_long_range_B_refined 4.922 r_long_range_B_other 4.922 r_scangle_other 2.249 r_mcangle_it 2.042 r_mcangle_other 2.042 r_angle_refined_deg 1.394 r_scbond_it 1.342 r_scbond_other 1.341 r_angle_other_deg 1.158 r_mcbond_it 1.146 r_mcbond_other 1.146 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.006 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 8276 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 131
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing