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Structure of D81A-Fructofuranosidase from Purpureocilum lilacinum in complex with raffinose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 0.1M Bis-Tris, pH 5.5 and 2M ammonium sulfate using 2:1 ratio (protein:reservoir). Cryoprotected with 20% glycerol and flash-cooled in liquid nitrogen.
Crystal Properties Matthews coefficient Solvent content 2.62 53.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.145 α = 90 b = 141.075 β = 90 c = 252.71 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2025-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979257 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 48.654 100 0.171 0.069 0.999 16.3 13.5 191260
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.02 100 0.531 0.704 2.3
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2 48.654 191149 9648 99.986 0.176 0.1746 0.1953 0.1783 29.472
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] 1.133 -0.403 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.028 r_dihedral_angle_2_deg 12.174 r_dihedral_angle_3_deg 11.206 r_dihedral_angle_1_deg 7.267 r_lrange_other 6.59 r_lrange_it 6.586 r_scangle_it 5.049 r_scangle_other 5.049 r_mcangle_it 3.856 r_mcangle_other 3.856
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.028 r_dihedral_angle_2_deg 12.174 r_dihedral_angle_3_deg 11.206 r_dihedral_angle_1_deg 7.267 r_lrange_other 6.59 r_lrange_it 6.586 r_scangle_it 5.049 r_scangle_other 5.049 r_mcangle_it 3.856 r_mcangle_other 3.856 r_scbond_it 3.395 r_scbond_other 3.395 r_mcbond_it 2.709 r_mcbond_other 2.708 r_angle_refined_deg 1.427 r_angle_other_deg 0.802 r_nbd_other 0.33 r_symmetry_nbd_refined 0.295 r_symmetry_nbd_other 0.217 r_nbd_refined 0.216 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.136 r_symmetry_xyhbond_nbd_refined 0.135 r_symmetry_xyhbond_nbd_other 0.133 r_symmetry_nbtor_other 0.126 r_chiral_restr 0.076 r_ncsr_local_group_1 0.062 r_ncsr_local_group_2 0.061 r_ncsr_local_group_3 0.059 r_ncsr_local_group_6 0.058 r_ncsr_local_group_4 0.057 r_ncsr_local_group_5 0.056 r_bond_other_d 0.016 r_gen_planes_other 0.011 r_gen_planes_refined 0.01 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16604 Nucleic Acid Atoms Solvent Atoms 1104 Heterogen Atoms 785
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing