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Crystal Structure of an Inositol hexakisphosphate kinase EhIP6KA in complexed with ATP and Ins(1,4,5)P3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4O4C PDB Entry 4O4C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 277 0.4 M NaH2PO4 in the presence of 10 mM ATP,5 mM IP3, 20 mM MgCl2. The crystals were further soaked under 22% (w/v) PEG 3350, 10 mM MgCl2, 10 mM ATP, 0.1 M sodium acetate, pH 5.2, 10 mM IP3 for 3 days. , VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.51 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.738 α = 90 b = 102.738 β = 90 c = 111.737 γ = 90
Symmetry Space Group I 41 2 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 MARMOSAIC 300 mm CCD 2013-06-03 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 Sym 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 2.1 50 99.4 0.086 29.1 6.7 17674 17674 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 100 0.551 3.4 6.2 875
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB Entry 4O4C 2.1 44.33 16743 16743 922 99.33 0.176 0.176 0.1734 0.2265 0.2092 RANDOM 39.271
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] -0.7 -0.7 1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.495 r_dihedral_angle_3_deg 14.945 r_dihedral_angle_4_deg 12.3 r_long_range_B_refined 7.022 r_long_range_B_other 6.932 r_dihedral_angle_1_deg 6.655 r_scangle_other 3.883 r_mcangle_other 3.153 r_mcangle_it 3.152 r_scbond_it 2.541
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.495 r_dihedral_angle_3_deg 14.945 r_dihedral_angle_4_deg 12.3 r_long_range_B_refined 7.022 r_long_range_B_other 6.932 r_dihedral_angle_1_deg 6.655 r_scangle_other 3.883 r_mcangle_other 3.153 r_mcangle_it 3.152 r_scbond_it 2.541 r_scbond_other 2.54 r_mcbond_it 2.082 r_mcbond_other 2.065 r_angle_refined_deg 1.705 r_angle_other_deg 0.827 r_chiral_restr 0.097 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2000 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 66
Software Software Software Name Purpose HKL-2000 data collection CCP4 model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CCP4 phasing