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Crystal Structure of an Inositol hexakisphosphate kinase EhIP6KA in complexed with ATP and Ins(1,3,4,5,6)P5
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 IP5 for 3 days, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.51 50.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.999 α = 90 b = 102.999 β = 90 c = 110.976 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 2013-03-01 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 1.9 50 99.3 0.049 42.9 8.1 23544 23544 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 1.9 1.93 93.9 0.527 2.6 6.3 1111
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB Entry 4O4C 1.9 28.86 22265 22265 1189 98.72 0.18505 0.18505 0.18328 0.1953 0.21926 0.2291 RANDOM 32.688
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] -0.79 -0.79 1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.085 r_dihedral_angle_3_deg 14.243 r_dihedral_angle_4_deg 13.488 r_long_range_B_refined 7.438 r_long_range_B_other 7.251 r_dihedral_angle_1_deg 6.625 r_scangle_other 3.743 r_mcangle_it 2.903 r_mcangle_other 2.902 r_scbond_it 2.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.085 r_dihedral_angle_3_deg 14.243 r_dihedral_angle_4_deg 13.488 r_long_range_B_refined 7.438 r_long_range_B_other 7.251 r_dihedral_angle_1_deg 6.625 r_scangle_other 3.743 r_mcangle_it 2.903 r_mcangle_other 2.902 r_scbond_it 2.307 r_scbond_other 2.29 r_mcbond_it 1.79 r_mcbond_other 1.789 r_angle_refined_deg 1.729 r_angle_other_deg 0.838 r_chiral_restr 0.133 r_bond_refined_d 0.011 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 2046 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 70
Software Software Software Name Purpose HKL-2000 data collection CCP4 model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CCP4 phasing