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Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with DL-6-deoxy-6-phosphoryloxymethyl-scyllo-inositol 1,2,4-trisphosphate/ADP/Mn
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W2C Chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 0.81 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl.
Protein:precipitant ratio 1:1.
Protein concentration: 17 mg/ml.
Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT.
Soaking overnight with 0.83 M sodium citrate, 0.1 M Tris pH 8.5, 0.1 M NaCl, 30 mM ligand, 3 mM ADP and 3 mM MnCl2. Cryoprotectant: Glycerol 30%.
Crystal Properties Matthews coefficient Solvent content 2.68 54.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.554 α = 90 b = 97.547 β = 90 c = 190.44 γ = 90
Symmetry Space Group C 2 2 21
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 6M KB mirrors, rectangular beam shape 2023-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979185 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) CC (Half) 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 58.28 95.4 0.014 1 22.8 13.2 80256 29
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.59 1.66 64.8 0.497 0.566 1.3 11.1
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 FOURIER SYNTHESIS THROUGHOUT 1.59 58.28 76237 4019 88.2 0.20191 0.19987 0.2087 0.24002 0.2497 RANDOM 37.876
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] 0.18 0.05 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.945 r_dihedral_angle_4_deg 16.183 r_dihedral_angle_3_deg 15.761 r_long_range_B_refined 6.889 r_long_range_B_other 6.787 r_dihedral_angle_1_deg 5.961 r_scangle_other 4.422 r_mcangle_other 3.558 r_mcangle_it 3.557 r_scbond_it 2.794
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.945 r_dihedral_angle_4_deg 16.183 r_dihedral_angle_3_deg 15.761 r_long_range_B_refined 6.889 r_long_range_B_other 6.787 r_dihedral_angle_1_deg 5.961 r_scangle_other 4.422 r_mcangle_other 3.558 r_mcangle_it 3.557 r_scbond_it 2.794 r_scbond_other 2.788 r_mcbond_it 2.328 r_mcbond_other 2.325 r_angle_other_deg 1.338 r_angle_refined_deg 1.315 r_chiral_restr 0.064 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.003 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 4296 Nucleic Acid Atoms Solvent Atoms 388 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling REFMAC phasing Coot model building PDB_EXTRACT data extraction