8PPG

Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with beta-D-glucopyranosyl 1,3,4,6-tetrakisphosphate/ADP/Mn after reaction


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 overnight with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 7 mM beta-D-glucopyranosyl 1,3,4-trisphosphate (substrate), 10 mM ATP and 10 mM MnCl2.
Crystal Properties
Matthews coefficientSolvent content
2.6353.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.283α = 90
b = 97.102β = 90
c = 190.755γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X CdTe 16MToroidal mirror, elliptical beam shape2022-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.8856ESRFID23-1

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
11.75190.761000.0240.99913.613.26705334.625
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)
11.751.781000.5720.6761.313.6

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 SYNTHESISTHROUGHOUT1.7595.3863607338699.980.207850.2060.2435RANDOM44.186
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]
3.12-0.99-2.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.936
r_dihedral_angle_3_deg16.913
r_dihedral_angle_4_deg16.792
r_long_range_B_refined7.896
r_long_range_B_other7.816
r_dihedral_angle_1_deg6.287
r_scangle_other5.869
r_mcangle_other4.722
r_mcangle_it4.72
r_scbond_it4.072
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.936
r_dihedral_angle_3_deg16.913
r_dihedral_angle_4_deg16.792
r_long_range_B_refined7.896
r_long_range_B_other7.816
r_dihedral_angle_1_deg6.287
r_scangle_other5.869
r_mcangle_other4.722
r_mcangle_it4.72
r_scbond_it4.072
r_scbond_other3.992
r_mcbond_it3.497
r_mcbond_other3.493
r_angle_refined_deg1.442
r_angle_other_deg1.346
r_chiral_restr0.073
r_bond_refined_d0.008
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 Atoms4144
Nucleic Acid Atoms
Solvent Atoms339
Heterogen Atoms158

Software

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