8PP8

Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with L-scyllo-inositol 1,2,4-trisphosphate/AMP-PNP/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 AMP-PNP and 3 mM MnCl2.
Crystal Properties
Matthews coefficientSolvent content
2.6954.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.561α = 90
b = 97.351β = 90
c = 191.177γ = 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
11.5995.5999.50.0150.99921.89.29016329.7
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)
11.591.6293.50.4470.591.25.3

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 SYNTHESISTHROUGHOUT1.5995.5985605454199.430.193570.192570.21218RANDOM37.629
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]
0.590.02-0.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.47
r_dihedral_angle_3_deg14.286
r_dihedral_angle_4_deg13.585
r_long_range_B_refined6.894
r_long_range_B_other6.809
r_dihedral_angle_1_deg6.004
r_scangle_other4.665
r_mcangle_other3.592
r_mcangle_it3.59
r_scbond_it2.971
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.47
r_dihedral_angle_3_deg14.286
r_dihedral_angle_4_deg13.585
r_long_range_B_refined6.894
r_long_range_B_other6.809
r_dihedral_angle_1_deg6.004
r_scangle_other4.665
r_mcangle_other3.592
r_mcangle_it3.59
r_scbond_it2.971
r_scbond_other2.94
r_mcbond_it2.346
r_mcbond_other2.34
r_angle_refined_deg1.378
r_angle_other_deg1.299
r_chiral_restr0.064
r_bond_refined_d0.006
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 Atoms4323
Nucleic Acid Atoms
Solvent Atoms422
Heterogen Atoms142

Software

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