6WOA

Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 2-Diphosphoinositol pentakisphosphate (2-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 Li2SO4, 25% (w/v) PEG 8000, 10% (v/v) isopropanol, 75mM NaAc, pH 5.5, 25 mM HEPES, pH 7.0, 20 mM MgCl2 and 80 mM NaF in present of 4mM 2-IP7
Crystal Properties
Matthews coefficientSolvent content
2.2545.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.496α = 90
b = 59.717β = 90
c = 61.887γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2020-02-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.0APS22-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.4650960.0740.0760.0179.616.730051
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)
11.461.4972.80.6440.6770.2020.8949

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 SYNTHESISTHROUGHOUT1.537.7125377128292.370.12980.12890.1481RANDOM16.703
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]
-2.931.071.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.237
r_dihedral_angle_4_deg11.53
r_dihedral_angle_3_deg11.394
r_dihedral_angle_1_deg7.583
r_rigid_bond_restr3.029
r_angle_refined_deg1.779
r_angle_other_deg1.437
r_chiral_restr0.12
r_bond_refined_d0.009
r_gen_planes_refined0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.237
r_dihedral_angle_4_deg11.53
r_dihedral_angle_3_deg11.394
r_dihedral_angle_1_deg7.583
r_rigid_bond_restr3.029
r_angle_refined_deg1.779
r_angle_other_deg1.437
r_chiral_restr0.12
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1086
Nucleic Acid Atoms
Solvent Atoms145
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
PHASERphasing