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Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 5-methylenebisphosphonate inositol pentakisphosphate (5-PCP-IP5)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 200 mM Li2SO4, 18% (w/v) PEG 8000, 5% (v/v) isopropanol, 100mM NaAc, pH 4.5
Crystal Properties Matthews coefficient Solvent content 2.13 42.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.802 α = 90 b = 59.544 β = 90 c = 62.526 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 CCD RAYONIX MX300-HS 2019-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM
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 1.5 50 99.3 0.045 0.049 0.017 13.5 8 27490
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 1.5 1.53 98.7 0.645 0.692 0.248 0.933 7.2
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 1.5 27.7 25093 1266 95.99 0.1524 0.1506 0.1513 0.1873 0.186 RANDOM 17.211
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] 1.18 2.15 -3.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.32 r_dihedral_angle_4_deg 17.635 r_dihedral_angle_3_deg 11.749 r_dihedral_angle_1_deg 7.182 r_rigid_bond_restr 6.395 r_angle_refined_deg 1.492 r_angle_other_deg 1.409 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.32 r_dihedral_angle_4_deg 17.635 r_dihedral_angle_3_deg 11.749 r_dihedral_angle_1_deg 7.182 r_rigid_bond_restr 6.395 r_angle_refined_deg 1.492 r_angle_other_deg 1.409 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1086 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction DENZO data reduction PHASER phasing