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Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with myo-5-PP-IP4, produced upon myo-(2OH)-IP5 phosphorylation by TvIPK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 296 10% w/v PEG8000, 10% v/v isopropanol, 200 mM lithium sulfate, 100 mM sodium acetate, pH 5.0, 5 mM IP6, soaked in 200 mM lithium chloride, 20% w/v PEG8000, 20% v/v isopropanol, 100 mM sodium acetate, pH 5.0, 20 mM magnesium chloride, 100 mM sodium fluoride in presence of TvIPK reaction solution with 2-OH-IP5
Crystal Properties Matthews coefficient Solvent content 2.47 50.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.304 α = 90 b = 59.64 β = 90 c = 62.698 γ = 90
Symmetry Space Group P 21 21 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 EIGER X 16M 2021-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.4 50 97.2 0.092 6 10.9 33485
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 79.9 0.645 0.681 0.213 0.916 7.8
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 1.4 36.1 31767 1668 96.93 0.15453 0.15375 0.154 0.1686 0.169 RANDOM 24.223
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] 3.05 -2.03 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.179 r_dihedral_angle_4_deg 15.873 r_dihedral_angle_3_deg 11.378 r_dihedral_angle_1_deg 7.087 r_long_range_B_refined 7.04 r_long_range_B_other 6.867 r_scangle_other 5.701 r_scbond_other 3.709 r_scbond_it 3.691 r_mcangle_other 2.686
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.179 r_dihedral_angle_4_deg 15.873 r_dihedral_angle_3_deg 11.378 r_dihedral_angle_1_deg 7.087 r_long_range_B_refined 7.04 r_long_range_B_other 6.867 r_scangle_other 5.701 r_scbond_other 3.709 r_scbond_it 3.691 r_mcangle_other 2.686 r_mcangle_it 2.684 r_angle_refined_deg 2.107 r_mcbond_it 1.809 r_mcbond_other 1.802 r_angle_other_deg 1.525 r_chiral_restr 0.152 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 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 1095 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling DENZO data reduction PHASER phasing