8G9D

Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 5- phosphonodifluoroacetamide inositol pentakisphosphate (5-PCF2Am-InsP5), an analogue of 5-InsP7


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental model 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529310% (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 200mM LiCl, 20% PEG8000, 20% isopropanol, 100mM HEPES 7.0, 20mM MgCl2 in the present of 2mM 5-PCF2Am-IP7
Crystal Properties
Matthews coefficientSolvent content
2.2244.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.444α = 90
b = 59.711β = 90
c = 62.402γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-11-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.000APS22-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
11.65098.90.08911.5623418
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6399.90.6515

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 SYNTHESISTHROUGHOUT1.631.6320338101490.270.192820.191180.22527RANDOM15.776
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg22.56
r_dihedral_angle_4_deg14.404
r_dihedral_angle_3_deg11.624
r_dihedral_angle_1_deg7.455
r_long_range_B_refined7.051
r_long_range_B_other6.975
r_scangle_other4.685
r_scbond_other3.024
r_scbond_it3.022
r_mcangle_other2.514
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg22.56
r_dihedral_angle_4_deg14.404
r_dihedral_angle_3_deg11.624
r_dihedral_angle_1_deg7.455
r_long_range_B_refined7.051
r_long_range_B_other6.975
r_scangle_other4.685
r_scbond_other3.024
r_scbond_it3.022
r_mcangle_other2.514
r_mcangle_it2.506
r_angle_refined_deg2.121
r_mcbond_it1.649
r_mcbond_other1.599
r_angle_other_deg1.582
r_chiral_restr0.195
r_bond_refined_d0.014
r_gen_planes_refined0.011
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 Atoms133
Heterogen Atoms41

Software

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