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Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with alpha-D-glucopyranosyl 1,3,4-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 0.84 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, 5 mM ligand, 3 mM ATP and 3 mM MnCl2.
Crystal Properties Matthews coefficient Solvent content 2.67 53.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.046 α = 90 b = 97.503 β = 90 c = 190.879 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 EIGER2 X CdTe 16M Toroidal mirror, elliptical beam shape 2021-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.774899 ESRF ID23-1
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 1.7 48.75 100 0.017 0.999 18.9 13.4 74155 33.244
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 1.7 1.73 100 0.453 0.663 1.7 14
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 1.7 47.77 70333 3765 99.98 0.19981 0.19818 0.2059 0.23069 0.2378 RANDOM 44.291
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] 1.41 -0.51 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.8 r_dihedral_angle_3_deg 14.768 r_dihedral_angle_4_deg 12.872 r_long_range_B_refined 7.72 r_long_range_B_other 7.681 r_dihedral_angle_1_deg 6.272 r_scangle_other 5.498 r_mcangle_other 4.584 r_mcangle_it 4.581 r_scbond_it 3.591
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.8 r_dihedral_angle_3_deg 14.768 r_dihedral_angle_4_deg 12.872 r_long_range_B_refined 7.72 r_long_range_B_other 7.681 r_dihedral_angle_1_deg 6.272 r_scangle_other 5.498 r_mcangle_other 4.584 r_mcangle_it 4.581 r_scbond_it 3.591 r_scbond_other 3.543 r_mcbond_it 3.14 r_mcbond_other 3.132 r_angle_refined_deg 1.388 r_angle_other_deg 1.304 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 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 4323 Nucleic Acid Atoms Solvent Atoms 338 Heterogen Atoms 123
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing Coot model building PDB_EXTRACT data extraction