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Crystal structure of the core catalytic domain of human inositol phosphate multikinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IF8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM MES Imidanzol buffer , pH 6.0, 50 mM beta-mercaptoethanol
Crystal Properties Matthews coefficient Solvent content 2.24 45.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.466 α = 90 b = 78.466 β = 90 c = 85.65 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 2016-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 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 1.8 50 99.4 0.114 15.5 8.7 25507
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 99.9 0.8 3.6 8.1
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 MOLECULAR REPLACEMENT THROUGHOUT 2if8 1.8 46.57 23558 1268 97.61 0.17287 0.17066 0.1796 0.21506 0.221 RANDOM 24.613
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] -0.06 -0.06 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.053 r_sphericity_free 33.75 r_dihedral_angle_4_deg 18.801 r_sphericity_bonded 17.659 r_dihedral_angle_3_deg 13.15 r_dihedral_angle_1_deg 6.578 r_long_range_B_refined 3.561 r_long_range_B_other 3.35 r_scangle_other 2.641 r_mcangle_other 2.282
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.053 r_sphericity_free 33.75 r_dihedral_angle_4_deg 18.801 r_sphericity_bonded 17.659 r_dihedral_angle_3_deg 13.15 r_dihedral_angle_1_deg 6.578 r_long_range_B_refined 3.561 r_long_range_B_other 3.35 r_scangle_other 2.641 r_mcangle_other 2.282 r_mcangle_it 2.276 r_scbond_other 2.052 r_scbond_it 2.047 r_rigid_bond_restr 1.649 r_mcbond_other 1.64 r_mcbond_it 1.638 r_angle_refined_deg 1.285 r_angle_other_deg 0.9 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 1906 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing