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Crystal structure of fructokinase with ADP and Fructose bound in the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EPQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 1.4 M Ammonium sulfate
0.1 M TRIS
10mM L-Fructose
20mM ADP, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 4.07 69.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.333 α = 90 b = 112.333 β = 90 c = 73.958 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 315 mirrors 2007-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 APS 19-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 2.45 40 100 0.11 24 10.6 20173 20173 2 2
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 2.45 2.49 100 0.71 3.5 9.5 989
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) 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 3EPQ 2.45 40 2 2 20093 19068 1024 99.87 0.15926 0.1573 0.1686 0.19619 0.1987 RANDOM 22.437
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] -0.81 -0.4 -0.81 1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.669 r_dihedral_angle_4_deg 17.254 r_dihedral_angle_3_deg 14.999 r_dihedral_angle_1_deg 6.233 r_scangle_it 4.782 r_scbond_it 2.975 r_angle_refined_deg 1.876 r_mcangle_it 1.794 r_angle_other_deg 0.965 r_mcbond_it 0.919
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.669 r_dihedral_angle_4_deg 17.254 r_dihedral_angle_3_deg 14.999 r_dihedral_angle_1_deg 6.233 r_scangle_it 4.782 r_scbond_it 2.975 r_angle_refined_deg 1.876 r_mcangle_it 1.794 r_angle_other_deg 0.965 r_mcbond_it 0.919 r_mcbond_other 0.204 r_chiral_restr 0.097 r_bond_refined_d 0.023 r_gen_planes_refined 0.008 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2252 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 45
Software Software Software Name Purpose SBC-Collect data collection MOLEMAN2 model building CCP4 model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLEMAN2 phasing CCP4 phasing