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Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with beta-D-glucopyranosyl 1,3,4,6-tetrakisphosphate/ADP/Mn after reaction
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 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 7 mM beta-D-glucopyranosyl 1,3,4-trisphosphate (substrate), 10 mM ATP and 10 mM MnCl2.
Crystal Properties Matthews coefficient Solvent content 2.63 53.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.283 α = 90 b = 97.102 β = 90 c = 190.755 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 2022-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8856 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 1.75 190.76 100 0.024 0.999 13.6 13.2 67053 34.625
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 1.75 1.78 100 0.572 0.676 1.3 13.6
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 1.75 95.38 63607 3386 99.98 0.20785 0.206 0.2138 0.2435 0.2463 RANDOM 44.186
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] 3.12 -0.99 -2.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.936 r_dihedral_angle_3_deg 16.913 r_dihedral_angle_4_deg 16.792 r_long_range_B_refined 7.896 r_long_range_B_other 7.816 r_dihedral_angle_1_deg 6.287 r_scangle_other 5.869 r_mcangle_other 4.722 r_mcangle_it 4.72 r_scbond_it 4.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.936 r_dihedral_angle_3_deg 16.913 r_dihedral_angle_4_deg 16.792 r_long_range_B_refined 7.896 r_long_range_B_other 7.816 r_dihedral_angle_1_deg 6.287 r_scangle_other 5.869 r_mcangle_other 4.722 r_mcangle_it 4.72 r_scbond_it 4.072 r_scbond_other 3.992 r_mcbond_it 3.497 r_mcbond_other 3.493 r_angle_refined_deg 1.442 r_angle_other_deg 1.346 r_chiral_restr 0.073 r_bond_refined_d 0.008 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 4144 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 158
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing Coot model building PDB_EXTRACT data extraction