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Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 5- phosphonodifluoroacetamide inositol pentakisphosphate (5-PCF2Am-InsP5), an analogue of 5-InsP7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 10% (w/v) PEG 8000, 10% (v/v) isopropanol, 200 mM Li2SO4, 75 mM NaAc, pH 5.5 and 25 mM HEPES, pH 7.0 and soaking in solution 200mM LiCl, 20% PEG8000, 20% isopropanol, 100mM HEPES 7.0, 20mM MgCl2 in the present of 2mM 5-PCF2Am-IP7
Crystal Properties Matthews coefficient Solvent content 2.22 44.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.444 α = 90 b = 59.711 β = 90 c = 62.402 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 2020-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 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 1.6 50 98.9 0.089 11.5 6 23418
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 99.9 0.651 5
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 1.6 31.63 20338 1014 90.27 0.19282 0.19118 0.205 0.22527 0.2302 RANDOM 15.776
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.56 r_dihedral_angle_4_deg 14.404 r_dihedral_angle_3_deg 11.624 r_dihedral_angle_1_deg 7.455 r_long_range_B_refined 7.051 r_long_range_B_other 6.975 r_scangle_other 4.685 r_scbond_other 3.024 r_scbond_it 3.022 r_mcangle_other 2.514
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.56 r_dihedral_angle_4_deg 14.404 r_dihedral_angle_3_deg 11.624 r_dihedral_angle_1_deg 7.455 r_long_range_B_refined 7.051 r_long_range_B_other 6.975 r_scangle_other 4.685 r_scbond_other 3.024 r_scbond_it 3.022 r_mcangle_other 2.514 r_mcangle_it 2.506 r_angle_refined_deg 2.121 r_mcbond_it 1.649 r_mcbond_other 1.599 r_angle_other_deg 1.582 r_chiral_restr 0.195 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 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 133 Heterogen Atoms 41
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement DENZO data reduction PHASER phasing