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Crystal Structure of Human CKIdelta with A86
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UYT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293.15 The construct used for crystallization was that of the wild type protein with the mutation R13N. Crystals of CK1d in complex with A-86 were obtained using hanging drop vapour diffusion set-ups. CK1d at a concentration of 13.6 mg/ml (50 mM HEPES, 266 mM NaCl, 1 mM EDTA, 1 mM DTT, 5 mM B-OG, pH 7.5) was pre-incubated with 2 mM (5.1-fold molar excess) of A-86 (150 mM in DMSO) for 1 h. 1 ul of the protein solution was then mixed with 1 ul of reservoir solution (0.1 M Na3-Citrate, pH 4.9, 18 %(w/v) PEG 3350) and equilibrated at 20 C over 0.4 ml of reservoir solution. Well diffracting crystals appeared over night
Crystal Properties Matthews coefficient Solvent content 2.29 46.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.232 α = 90 b = 73.659 β = 103.57 c = 89.204 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 110.15 PIXEL DECTRIS PILATUS3 2M 2016-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
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 1.59 29.19 96.5 0.09 7.1 2.4 80180
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 1.59 1.68 96.4 0.57 2.4
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 3uyt 1.59 29.19 75238 3911 95.1 0.19153 0.18869 0.2025 0.24976 0.2646 RANDOM 28.076
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] -0.44 -0.39 2.91 -2.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.786 r_dihedral_angle_3_deg 14.524 r_dihedral_angle_4_deg 12.634 r_long_range_B_refined 10.403 r_long_range_B_other 9.764 r_dihedral_angle_1_deg 6.179 r_scangle_other 5.251 r_mcangle_it 3.838 r_mcangle_other 3.837 r_scbond_it 3.513
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.786 r_dihedral_angle_3_deg 14.524 r_dihedral_angle_4_deg 12.634 r_long_range_B_refined 10.403 r_long_range_B_other 9.764 r_dihedral_angle_1_deg 6.179 r_scangle_other 5.251 r_mcangle_it 3.838 r_mcangle_other 3.837 r_scbond_it 3.513 r_scbond_other 3.512 r_mcbond_it 2.767 r_mcbond_other 2.767 r_angle_refined_deg 1.533 r_angle_other_deg 0.985 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 4788 Nucleic Acid Atoms Solvent Atoms 832 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement SCALA data scaling