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Crystal structure of GH9l Inulin fructotransferases (IFTase) in compex with fruetosyl nystose (GF4)
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 53.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.713 α = 90 b = 167.713 β = 90 c = 85.16 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 1.96 50 96.2 0.076 18.2 5.7 94026
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 1.96 1.99 0.452 3.277
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 (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 1.96 42.12 89022 4693 95.86 0.15996 0.15864 0.17 0.18469 0.1976 RANDOM 33.193
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.276 r_dihedral_angle_4_deg 18.476 r_dihedral_angle_3_deg 12.478 r_dihedral_angle_1_deg 8.085 r_long_range_B_refined 4.546 r_long_range_B_other 4.526 r_scangle_other 3.764 r_scbond_it 2.599 r_scbond_other 2.599 r_mcangle_it 2.536
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.276 r_dihedral_angle_4_deg 18.476 r_dihedral_angle_3_deg 12.478 r_dihedral_angle_1_deg 8.085 r_long_range_B_refined 4.546 r_long_range_B_other 4.526 r_scangle_other 3.764 r_scbond_it 2.599 r_scbond_other 2.599 r_mcangle_it 2.536 r_mcangle_other 2.536 r_angle_other_deg 2.505 r_mcbond_it 1.956 r_mcbond_other 1.955 r_angle_refined_deg 1.609 r_chiral_restr 0.063 r_bond_other_d 0.035 r_gen_planes_other 0.009 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 9080 Nucleic Acid Atoms Solvent Atoms 423 Heterogen Atoms 381
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling RESOLVE phasing