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Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with myo-5-IP7, produced upon myo-IP6 phosphorylation by TvI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 297 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 myo-IP6
Crystal Properties Matthews coefficient Solvent content 2.46 49.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.995 α = 90 b = 59.597 β = 90 c = 62.695 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 2021-10-29 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 1.55 50 96.8 0.144 4.9 9.4 24404
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 1.55 1.58 82.9 0.42 0.464 0.193 0.892 4.9
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 1.55 35.94 23137 1230 96.86 0.16276 0.16142 0.1702 0.18782 0.1915 RANDOM 22.894
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] -0.06 0.05 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.842 r_dihedral_angle_4_deg 17.967 r_dihedral_angle_3_deg 13.441 r_long_range_B_refined 7.4 r_long_range_B_other 7.276 r_dihedral_angle_1_deg 7.192 r_scangle_other 6.355 r_scbond_other 4.124 r_scbond_it 4.114 r_mcangle_it 2.573
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.842 r_dihedral_angle_4_deg 17.967 r_dihedral_angle_3_deg 13.441 r_long_range_B_refined 7.4 r_long_range_B_other 7.276 r_dihedral_angle_1_deg 7.192 r_scangle_other 6.355 r_scbond_other 4.124 r_scbond_it 4.114 r_mcangle_it 2.573 r_mcangle_other 2.572 r_angle_refined_deg 2.242 r_mcbond_it 1.763 r_mcbond_other 1.763 r_angle_other_deg 1.507 r_chiral_restr 0.233 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 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 164 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling DENZO data reduction PHASER phasing