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Crystal structure of GH9l Inulinfructotransferases (IFTase) in complex with GF2
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 53.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.58 α = 90 b = 167.58 β = 90 c = 85.478 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 2.2 50 100 0.067 23.48 5.7 69363
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 2.2 2.24 0.488 2.14
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 2.201 48.423 69296 3508 99.885 0.148 0.1462 0.1568 0.1843 0.1924 33.899
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] -0.018 -0.009 -0.018 0.059
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.824 r_dihedral_angle_4_deg 19.72 r_dihedral_angle_3_deg 13.129 r_dihedral_angle_1_deg 8.203 r_lrange_it 4.184 r_lrange_other 4.124 r_scangle_it 2.889 r_scangle_other 2.889 r_mcangle_it 2.21 r_mcangle_other 2.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.824 r_dihedral_angle_4_deg 19.72 r_dihedral_angle_3_deg 13.129 r_dihedral_angle_1_deg 8.203 r_lrange_it 4.184 r_lrange_other 4.124 r_scangle_it 2.889 r_scangle_other 2.889 r_mcangle_it 2.21 r_mcangle_other 2.21 r_scbond_it 1.99 r_scbond_other 1.988 r_mcbond_it 1.569 r_mcbond_other 1.567 r_angle_refined_deg 1.433 r_angle_other_deg 1.221 r_nbd_other 0.249 r_nbd_refined 0.185 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.149 r_xyhbond_nbd_refined 0.14 r_symmetry_xyhbond_nbd_refined 0.126 r_symmetry_nbd_refined 0.11 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.055 r_symmetry_xyhbond_nbd_other 0.03 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9081 Nucleic Acid Atoms Solvent Atoms 547 Heterogen Atoms 204
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling RESOLVE phasing