6WOB

Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 4-diphosphoinositol pentakisphosphate (4-IP7), Mg, and Fluoride ion


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629310% (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 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 4-IP7
Crystal Properties
Matthews coefficientSolvent content
2.1242.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.607α = 90
b = 59.541β = 90
c = 62.47γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-07-11MSINGLE 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)Rrim I (All)Rpim I (All)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
11.455099.10.0580.0620.02110.98.130058
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)
11.451.48910.550.5970.2250.8845.8

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 SYNTHESISTHROUGHOUT1.4531.0126157134390.850.16220.16020.2028RANDOM17.64
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]
-5.062.692.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.851
r_dihedral_angle_4_deg18.576
r_rigid_bond_restr14.371
r_dihedral_angle_3_deg12.68
r_dihedral_angle_1_deg7.302
r_angle_refined_deg1.91
r_angle_other_deg1.448
r_chiral_restr0.215
r_bond_refined_d0.013
r_gen_planes_refined0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.851
r_dihedral_angle_4_deg18.576
r_rigid_bond_restr14.371
r_dihedral_angle_3_deg12.68
r_dihedral_angle_1_deg7.302
r_angle_refined_deg1.91
r_angle_other_deg1.448
r_chiral_restr0.215
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1086
Nucleic Acid Atoms
Solvent Atoms133
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
PHASERphasing