6M88

Crystal structure of the core catalytic domain of human inositol phosphate multikinase in complex with myricetin


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629835% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM MES Imidanzol buffer , pH 6.0, 50 mM beta-mercaptoethanol at 298K. To obtain complex structure, the apo crystal was further soaked under 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM HEPES, pH 7.5 at 298K in the presence of 2 mM myricetin for 3 days.
Crystal Properties
Matthews coefficientSolvent content
2.1743.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.717α = 90
b = 77.717β = 90
c = 84.465γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2018-04-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1APS22-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
11.95099.60.1230.130.040.97716.99.72093916.83
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)
11.91.931000.7280.7680.2410.8849.6

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 SYNTHESISTHROUGHOUT5w2g1.95019777106899.320.176890.173370.24428RANDOM24.725
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]
-0.24-0.240.47
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free43.736
r_dihedral_angle_2_deg36.511
r_sphericity_bonded22.157
r_dihedral_angle_4_deg13.652
r_dihedral_angle_3_deg12.921
r_dihedral_angle_1_deg6.457
r_long_range_B_refined4.953
r_long_range_B_other4.789
r_mcangle_it3.29
r_mcangle_other3.289
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free43.736
r_dihedral_angle_2_deg36.511
r_sphericity_bonded22.157
r_dihedral_angle_4_deg13.652
r_dihedral_angle_3_deg12.921
r_dihedral_angle_1_deg6.457
r_long_range_B_refined4.953
r_long_range_B_other4.789
r_mcangle_it3.29
r_mcangle_other3.289
r_scangle_other3.114
r_scbond_it2.394
r_scbond_other2.393
r_mcbond_it2.371
r_mcbond_other2.37
r_rigid_bond_restr1.487
r_angle_refined_deg1.31
r_angle_other_deg0.907
r_chiral_restr0.071
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1935
Nucleic Acid Atoms
Solvent Atoms177
Heterogen Atoms23

Software

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