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Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 5-Diphosphoinositol pentakisphosphate (5-IP7), Mg, and Fluoride ion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FVV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 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 condition of 200 mM LiCl, 20% (w/v) PEG 8000, 20% (v/v) isopropanol, 100 mM HEPES, pH 7.0, 20 mM MgCl2 and 80 mM NaF in present of 2mM 5-IP7
Crystal Properties Matthews coefficient Solvent content 2.16 43.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.365 α = 90 b = 59.602 β = 90 c = 62.493 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 2019-06-08 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) Rrim I (All) Rpim I (All) 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 98.9 0.075 0.077 0.02 9.6 14.3 33828
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 86.9 0.637 0.668 0.196 0.933 10
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2FVV 1.4 43.13 30106 1575 92.44 0.1403 0.139 0.1406 0.168 0.1691 RANDOM 16.167
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] -2.01 2.52 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.084 r_dihedral_angle_4_deg 16.872 r_dihedral_angle_3_deg 9.933 r_dihedral_angle_1_deg 7.342 r_rigid_bond_restr 5.874 r_angle_refined_deg 1.814 r_angle_other_deg 1.432 r_chiral_restr 0.214 r_bond_refined_d 0.01 r_gen_planes_refined 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.084 r_dihedral_angle_4_deg 16.872 r_dihedral_angle_3_deg 9.933 r_dihedral_angle_1_deg 7.342 r_rigid_bond_restr 5.874 r_angle_refined_deg 1.814 r_angle_other_deg 1.432 r_chiral_restr 0.214 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1086 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data processing DENZO data reduction PHASER phasing