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Crystal structure of GH9l Inulin fructotransferases(IFTase)incomplex with nystose(F3)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VHT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.2 M lithium sulfate monohydrate
0.1 M Tris (pH 8.5)
25% (w/v) polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.67 53.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.642 α = 90 b = 167.642 β = 90 c = 85.297 γ = 120
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 RIGAKU SATURN 944+ 2014-12-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54178
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 2.8 50 100 0.155 11.22 5.4 33668
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 2.8 2.85 0.495
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.803 48.441 33625 1701 99.736 0.161 0.1582 0.1625 0.2079 0.2071 31.522
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] 0.011 0.005 0.011 -0.034
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.315 r_dihedral_angle_4_deg 20.335 r_dihedral_angle_3_deg 15.856 r_dihedral_angle_1_deg 8.325 r_lrange_it 5.091 r_lrange_other 5.091 r_scangle_it 3.588 r_scangle_other 3.588 r_mcangle_it 2.892 r_mcangle_other 2.892
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.315 r_dihedral_angle_4_deg 20.335 r_dihedral_angle_3_deg 15.856 r_dihedral_angle_1_deg 8.325 r_lrange_it 5.091 r_lrange_other 5.091 r_scangle_it 3.588 r_scangle_other 3.588 r_mcangle_it 2.892 r_mcangle_other 2.892 r_scbond_it 2.428 r_scbond_other 2.428 r_mcbond_it 1.871 r_mcbond_other 1.871 r_angle_refined_deg 1.772 r_angle_other_deg 1.2 r_nbd_other 0.235 r_nbd_refined 0.194 r_symmetry_nbd_other 0.191 r_symmetry_xyhbond_nbd_refined 0.17 r_nbtor_refined 0.154 r_symmetry_nbd_refined 0.147 r_xyhbond_nbd_refined 0.142 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.061 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9081 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 293
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling RESOLVE phasing