8T8Z

Crystal structure of Terrestrivirus Inositol pyrophosphatase kinase in complex with ADP and myo-(1OH)IP5


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP727712% PEG8000, 100mM HEPES pH 7.0, 10mM NaH2PO4, 10% Ethylene Glycol, 5mM ADP and 10mM MgCl2, then soaked in 25% PEG8000, 100mM HEPES pH 7.0, 20% Ethylene Glycol with 5mM myo-(1OH)-IP5, 5mM ADP and 10mM MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.856.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.841α = 90
b = 103.835β = 90
c = 102.719γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-10-14MSINGLE 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)CC (Half)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
12.65099.40.0910.0980.0360.9958.67.110770
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)
12.62.6498.80.6920.7480.2730.7546.9

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 SYNTHESISTHROUGHOUT2.646.38961552593.660.177610.174470.2347RANDOM38.373
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]
-0.070.020.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.174
r_dihedral_angle_4_deg24.34
r_dihedral_angle_3_deg17.522
r_long_range_B_other7.917
r_long_range_B_refined7.915
r_dihedral_angle_1_deg7.652
r_scangle_other5.903
r_mcangle_other4.607
r_mcangle_it4.602
r_scbond_it3.807
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.174
r_dihedral_angle_4_deg24.34
r_dihedral_angle_3_deg17.522
r_long_range_B_other7.917
r_long_range_B_refined7.915
r_dihedral_angle_1_deg7.652
r_scangle_other5.903
r_mcangle_other4.607
r_mcangle_it4.602
r_scbond_it3.807
r_scbond_other3.776
r_mcbond_it2.88
r_mcbond_other2.845
r_angle_refined_deg1.616
r_angle_other_deg1.277
r_chiral_restr0.079
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms1772
Nucleic Acid Atoms
Solvent Atoms58
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing