8TF9

Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with myo-5-IP7, produced upon myo-IP6 phosphorylation by TvI


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP529710% 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 coefficientSolvent content
2.4649.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.995α = 90
b = 59.597β = 90
c = 62.695γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-10-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.555096.80.1444.99.424404
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)RedundancyNumber Unique Reflections (All)
11.551.5882.90.420.4640.1930.8924.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1.5535.9423137123096.860.162760.161420.18782RANDOM22.894
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]
-0.060.050.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.842
r_dihedral_angle_4_deg17.967
r_dihedral_angle_3_deg13.441
r_long_range_B_refined7.4
r_long_range_B_other7.276
r_dihedral_angle_1_deg7.192
r_scangle_other6.355
r_scbond_other4.124
r_scbond_it4.114
r_mcangle_it2.573
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.842
r_dihedral_angle_4_deg17.967
r_dihedral_angle_3_deg13.441
r_long_range_B_refined7.4
r_long_range_B_other7.276
r_dihedral_angle_1_deg7.192
r_scangle_other6.355
r_scbond_other4.124
r_scbond_it4.114
r_mcangle_it2.573
r_mcangle_other2.572
r_angle_refined_deg2.242
r_mcbond_it1.763
r_mcbond_other1.763
r_angle_other_deg1.507
r_chiral_restr0.233
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
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 AtomsNumber
Protein Atoms1095
Nucleic Acid Atoms
Solvent Atoms164
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing