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Crystal Structure of an Inositol hexakisphosphate kinase EhIP6KA in complexed with ATP and InsP6
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, 20 mM IP6 for 3 days, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.44 49.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.229 α = 90 b = 102.229 β = 90 c = 109.493 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 2013-03-31 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 1.7 50 96.4 0.053 56.7 9.8 31175 31175 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 1.7 1.73 71.6 0.54 2.4 5.2 1145
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 1.7 34.4 29589 29589 1568 96.13 0.19277 0.19277 0.19129 0.1978 0.2218 0.2259 RANDOM 32.582
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] -0.92 -0.92 1.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.396 r_dihedral_angle_4_deg 14.141 r_dihedral_angle_3_deg 13.525 r_long_range_B_refined 6.672 r_long_range_B_other 6.511 r_dihedral_angle_1_deg 6.494 r_scangle_other 3.077 r_mcangle_it 2.571 r_mcangle_other 2.57 r_scbond_it 1.881
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.396 r_dihedral_angle_4_deg 14.141 r_dihedral_angle_3_deg 13.525 r_long_range_B_refined 6.672 r_long_range_B_other 6.511 r_dihedral_angle_1_deg 6.494 r_scangle_other 3.077 r_mcangle_it 2.571 r_mcangle_other 2.57 r_scbond_it 1.881 r_scbond_other 1.876 r_angle_refined_deg 1.825 r_mcbond_other 1.564 r_mcbond_it 1.563 r_angle_other_deg 1.016 r_chiral_restr 0.399 r_bond_refined_d 0.01 r_bond_other_d 0.006 r_gen_planes_refined 0.006 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 190 Heterogen Atoms 79
Software Software Software Name Purpose HKL-2000 data collection CCP4 model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CCP4 phasing