8PP9

Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with scyllo-inositol 1,2,3,5-tetrakisphosphate/ADP/Mn


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1W2CChain A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52910.81 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 17 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking 2h with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 5 mM ligand, 3 mM ADP and 3 mM MnCl2.
Crystal Properties
Matthews coefficientSolvent content
2.6954.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.504α = 90
b = 97.509β = 90
c = 191.487γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKB mirrors, rectangular beam shape2022-02-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.999871ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.7358.181000.0210.99917.59.77086832.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.731.7699.90.4390.6271.48.4

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 SYNTHESISTHROUGHOUT1.7358.1867349348799.910.194620.193810.20989RANDOM39.609
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]
2.01-1.13-0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.117
r_dihedral_angle_3_deg15.477
r_dihedral_angle_4_deg14.84
r_long_range_B_refined7.65
r_long_range_B_other7.543
r_dihedral_angle_1_deg6.302
r_scangle_other5.206
r_mcangle_other4.025
r_mcangle_it4.022
r_scbond_it3.376
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.117
r_dihedral_angle_3_deg15.477
r_dihedral_angle_4_deg14.84
r_long_range_B_refined7.65
r_long_range_B_other7.543
r_dihedral_angle_1_deg6.302
r_scangle_other5.206
r_mcangle_other4.025
r_mcangle_it4.022
r_scbond_it3.376
r_scbond_other3.328
r_mcbond_it2.797
r_mcbond_other2.783
r_angle_refined_deg1.433
r_angle_other_deg1.293
r_chiral_restr0.068
r_bond_refined_d0.007
r_gen_planes_refined0.007
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 Atoms4211
Nucleic Acid Atoms
Solvent Atoms425
Heterogen Atoms142

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
REFMACphasing
Cootmodel building
PDB_EXTRACTdata extraction