6WOG

Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 5-methylenebisphosphonate inositol pentakisphosphate (5-PCP-IP5)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.5293200 mM Li2SO4, 18% (w/v) PEG 8000, 5% (v/v) isopropanol, 100mM NaAc, pH 4.5
Crystal Properties
Matthews coefficientSolvent content
2.1342.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.802α = 90
b = 59.544β = 90
c = 62.526γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2019-06-07MSINGLE 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
11.55099.30.0450.0490.01713.5827490
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)
11.51.5398.70.6450.6920.2480.9337.2

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 SYNTHESISTHROUGHOUT1.527.725093126695.990.15240.15060.1873RANDOM17.211
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]
1.182.15-3.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.32
r_dihedral_angle_4_deg17.635
r_dihedral_angle_3_deg11.749
r_dihedral_angle_1_deg7.182
r_rigid_bond_restr6.395
r_angle_refined_deg1.492
r_angle_other_deg1.409
r_chiral_restr0.081
r_bond_refined_d0.009
r_gen_planes_refined0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.32
r_dihedral_angle_4_deg17.635
r_dihedral_angle_3_deg11.749
r_dihedral_angle_1_deg7.182
r_rigid_bond_restr6.395
r_angle_refined_deg1.492
r_angle_other_deg1.409
r_chiral_restr0.081
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1086
Nucleic Acid Atoms
Solvent Atoms121
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
PHASERphasing