6WO7

Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 5-Diphosphoinositol pentakisphosphate (5-IP7), Mg, and Fluoride ion


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FVV 

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 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 coefficientSolvent content
2.1643.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.365α = 90
b = 59.602β = 90
c = 62.493γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-06-08MSINGLE 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
11.45098.90.0750.0770.029.614.333828
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)
11.41.4286.90.6370.6680.1960.93310

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 SYNTHESISTHROUGHOUT2FVV1.443.1330106157592.440.14030.1390.168RANDOM16.167
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]
-2.012.52-0.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.084
r_dihedral_angle_4_deg16.872
r_dihedral_angle_3_deg9.933
r_dihedral_angle_1_deg7.342
r_rigid_bond_restr5.874
r_angle_refined_deg1.814
r_angle_other_deg1.432
r_chiral_restr0.214
r_bond_refined_d0.01
r_gen_planes_refined0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.084
r_dihedral_angle_4_deg16.872
r_dihedral_angle_3_deg9.933
r_dihedral_angle_1_deg7.342
r_rigid_bond_restr5.874
r_angle_refined_deg1.814
r_angle_other_deg1.432
r_chiral_restr0.214
r_bond_refined_d0.01
r_gen_planes_refined0.007
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 Atoms172
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data processing
DENZOdata reduction
PHASERphasing