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Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with DL-6-deoxy-6-hydroxy-methyl-scyllo-inositol 1,2,4-trisphosphate/ATP/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 0.83 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl.
Protein:precipitant ratio 1:1.
Protein concentration: 18 mg/ml.
Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT.
Soaking 2h with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 10 mM ligand, 3 mM ATP and 3 mM MnCl2.
Crystal Properties Matthews coefficient Solvent content 2.69 54.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.16 α = 90 b = 97.524 β = 90 c = 192.056 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 2021-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979178 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 1.77 48.01 99.7 0.024 0.998 16 11 66119 30.204
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 1.77 1.81 98 0.427 0.607 1.6 9.8
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 1.77 47.31 62730 3335 99.65 0.20331 0.20191 0.2102 0.23047 0.2333 RANDOM 39.839
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] 1.18 -0.09 -1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.97 r_dihedral_angle_4_deg 17.031 r_dihedral_angle_3_deg 16.255 r_long_range_B_refined 7.464 r_long_range_B_other 7.436 r_dihedral_angle_1_deg 6.531 r_scangle_other 4.898 r_mcangle_it 3.949 r_mcangle_other 3.949 r_scbond_it 3.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.97 r_dihedral_angle_4_deg 17.031 r_dihedral_angle_3_deg 16.255 r_long_range_B_refined 7.464 r_long_range_B_other 7.436 r_dihedral_angle_1_deg 6.531 r_scangle_other 4.898 r_mcangle_it 3.949 r_mcangle_other 3.949 r_scbond_it 3.116 r_scbond_other 3.106 r_mcbond_it 2.69 r_mcbond_other 2.686 r_angle_refined_deg 1.358 r_angle_other_deg 1.293 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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 4230 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms 149
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing Coot model building PDB_EXTRACT data extraction