5W2H

Crystal structure of the core catalytic domain of human inositol phosphate multikinase in complex with Ins(1,4,5)P3 and ADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5W2G 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29835% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM MES Imidanzol buffer , pH 6.0, 50 mM beta-mercaptoethanol.To obtain complex structures, the apo crystal were further soaked under 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM HEPES, pH 7.5 at 298K in the presence of 20 mM Ins(1,4,5)P3, 10 mM Mg and 5mM ATP for 1 day.
Crystal Properties
Matthews coefficientSolvent content
2.2244.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.015α = 90
b = 78.015β = 90
c = 85.915γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2016-08-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1APS22-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.95099.90.10918921557
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.931000.8970.3173.38.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 SYNTHESISTHROUGHOUT5W2G1.932.3520189108298.660.166660.163430.22952RANDOM25.704
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]
-0.02-0.020.05
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free43.63
r_dihedral_angle_2_deg33.825
r_dihedral_angle_4_deg14.122
r_dihedral_angle_3_deg14.031
r_sphericity_bonded13.429
r_dihedral_angle_1_deg6.509
r_long_range_B_refined5.122
r_long_range_B_other4.541
r_scangle_other3.262
r_rigid_bond_restr2.966
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free43.63
r_dihedral_angle_2_deg33.825
r_dihedral_angle_4_deg14.122
r_dihedral_angle_3_deg14.031
r_sphericity_bonded13.429
r_dihedral_angle_1_deg6.509
r_long_range_B_refined5.122
r_long_range_B_other4.541
r_scangle_other3.262
r_rigid_bond_restr2.966
r_scbond_it2.965
r_scbond_other2.963
r_mcangle_other2.323
r_mcangle_it2.32
r_mcbond_it1.685
r_mcbond_other1.685
r_angle_refined_deg1.538
r_angle_other_deg0.758
r_chiral_restr0.08
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1935
Nucleic Acid Atoms
Solvent Atoms172
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling