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Crystal structure of the core catalytic domain of human inositol phosphate multikinase in complex with an inhibitor UNC7844
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5W2I
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 5 mM compound for 3 days
Crystal Properties Matthews coefficient Solvent content 2.18 43.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.238 α = 90 b = 78.238 β = 90 c = 85.008 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 2020-03-21 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) 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 1.646 50 99.7 0.056 44.08 11.3 32550
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 0.908 0.837 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1.646 37.376 32385 1629 99.225 0.218 0.2157 0.2302 0.2563 0.2674 23.624
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] 0.105 0.105 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.277 r_dihedral_angle_3_deg 13.27 r_dihedral_angle_2_deg 8.743 r_lrange_it 8.435 r_lrange_other 7.356 r_dihedral_angle_1_deg 6.605 r_rigid_bond_restr 2.416 r_angle_refined_deg 1.87 r_scangle_it 1.823 r_scangle_other 1.822
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.277 r_dihedral_angle_3_deg 13.27 r_dihedral_angle_2_deg 8.743 r_lrange_it 8.435 r_lrange_other 7.356 r_dihedral_angle_1_deg 6.605 r_rigid_bond_restr 2.416 r_angle_refined_deg 1.87 r_scangle_it 1.823 r_scangle_other 1.822 r_mcangle_it 1.786 r_mcangle_other 1.786 r_scbond_it 1.129 r_scbond_other 1.128 r_mcbond_it 1.016 r_mcbond_other 1.016 r_angle_other_deg 0.61 r_symmetry_xyhbond_nbd_refined 0.258 r_nbd_refined 0.23 r_nbd_other 0.225 r_xyhbond_nbd_refined 0.21 r_symmetry_nbd_other 0.2 r_nbtor_refined 0.19 r_symmetry_nbd_refined 0.177 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.081 r_xyhbond_nbd_other 0.055 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_symmetry_xyhbond_nbd_other 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1943 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling