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Crystal structure of the core catalytic domain of human inositol phosphate multikinase in complex with rhamnetin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5W2G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 35% (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 10 mM rhametine for 3 days.
Crystal Properties Matthews coefficient Solvent content 2.22 44.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.152 α = 90 b = 78.152 β = 90 c = 85.562 γ = 90
Symmetry Space Group P 42 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX300-HS 2017-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2 50 99.5 0.074 0.077 0.02 29.8 13.2 18331
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) Redundancy Number Unique Reflections (All) 1 2 2.03 100 0.801 0.833 0.222 0.901 3.5 13.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 5w2g 2 50 17229 943 98.6 0.18729 0.18431 0.1938 0.24508 0.2507 RANDOM 30.315
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] 1.17 1.17 -2.34
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 44.322 r_dihedral_angle_2_deg 34.577 r_sphericity_bonded 24.109 r_dihedral_angle_4_deg 18.097 r_dihedral_angle_3_deg 13.684 r_dihedral_angle_1_deg 6.282 r_long_range_B_refined 4.111 r_long_range_B_other 4.108 r_mcangle_other 2.606 r_mcangle_it 2.605
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 44.322 r_dihedral_angle_2_deg 34.577 r_sphericity_bonded 24.109 r_dihedral_angle_4_deg 18.097 r_dihedral_angle_3_deg 13.684 r_dihedral_angle_1_deg 6.282 r_long_range_B_refined 4.111 r_long_range_B_other 4.108 r_mcangle_other 2.606 r_mcangle_it 2.605 r_scangle_other 2.583 r_scbond_it 1.945 r_scbond_other 1.932 r_mcbond_it 1.917 r_mcbond_other 1.912 r_angle_refined_deg 1.255 r_angle_other_deg 0.881 r_rigid_bond_restr 0.72 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 1941 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling