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Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with beta-D-glucopyranosylmethanol 3,4,6,1'-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 0.80 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-glucopyranosylmethanol 3,4,1'-trisphosphate (substrate), 10 mM ATP and 10 mM MnCl2.
Crystal Properties Matthews coefficient Solvent content 2.68 54.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.53 α = 90 b = 97.063 β = 90 c = 191.127 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 1.75 191.13 99.9 0.023 0.999 16.6 13.6 68270 29.4
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 99.9 0.467 0.661 1.6 14.2
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 95.56 64763 3449 99.93 0.1989 0.19706 0.2063 0.23423 0.2412 RANDOM 40.128
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] 1.59 -0.49 -1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.325 r_dihedral_angle_3_deg 16.055 r_dihedral_angle_4_deg 15.259 r_long_range_B_refined 7.268 r_long_range_B_other 7.191 r_dihedral_angle_1_deg 6.178 r_scangle_other 4.651 r_mcangle_other 3.791 r_mcangle_it 3.79 r_scbond_it 2.989
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.325 r_dihedral_angle_3_deg 16.055 r_dihedral_angle_4_deg 15.259 r_long_range_B_refined 7.268 r_long_range_B_other 7.191 r_dihedral_angle_1_deg 6.178 r_scangle_other 4.651 r_mcangle_other 3.791 r_mcangle_it 3.79 r_scbond_it 2.989 r_scbond_other 2.922 r_mcbond_it 2.5 r_mcbond_other 2.495 r_angle_refined_deg 1.348 r_angle_other_deg 1.265 r_chiral_restr 0.062 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 4279 Nucleic Acid Atoms Solvent Atoms 403 Heterogen Atoms 156
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling REFMAC phasing Coot model building PDB_EXTRACT data extraction