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Crystal structure of human Casein Kinase I delta in complex with a photoswitchable 2-Azoimidazole-based Inhibitor (compound 3)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MQV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Ammonium citrate tribasic pH 7.0
20 % w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.1 41.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.819 α = 90 b = 72.223 β = 103.21 c = 89.161 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 PILATUS 2M-F 2018-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.000021 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.039 46.39 98.29 12.76 8.2 37921
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.039 2.112
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5MQV 2.039 47.527 1.44 37898 1890 98.28 0.1869 0.1853 0.1881 0.219 0.2212
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.047 f_angle_d 0.734 f_chiral_restr 0.045 f_bond_d 0.005 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4563 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 96
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing