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Structure of D81A-Fructofuranosidase from Purpureocilum lilacinum in complex with sucrose
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 2.73 54.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.104 α = 90 b = 141.122 β = 90 c = 252.658 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 2025-05-14 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 49.408 99.9 0.129 0.055 0.999 16.1 12.5 189994
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 2.04 97.9 0.56 0.59 1.9 12.4
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 THROUGHOUT 2.004 49.408 189881 9588 99.897 0.18 0.1792 0.1872 0.1977 0.2068 34.537
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] 1.487 -0.413 -1.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.21 r_dihedral_angle_3_deg 10.912 r_dihedral_angle_2_deg 8.996 r_dihedral_angle_1_deg 7.456 r_lrange_other 7.108 r_lrange_it 7.106 r_scangle_it 5.314 r_scangle_other 5.314 r_mcangle_it 4.19 r_mcangle_other 4.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.21 r_dihedral_angle_3_deg 10.912 r_dihedral_angle_2_deg 8.996 r_dihedral_angle_1_deg 7.456 r_lrange_other 7.108 r_lrange_it 7.106 r_scangle_it 5.314 r_scangle_other 5.314 r_mcangle_it 4.19 r_mcangle_other 4.19 r_scbond_it 3.549 r_scbond_other 3.548 r_mcbond_it 2.938 r_mcbond_other 2.938 r_angle_refined_deg 1.38 r_angle_other_deg 0.526 r_symmetry_nbd_refined 0.354 r_nbd_other 0.297 r_symmetry_nbd_other 0.21 r_nbd_refined 0.202 r_symmetry_xyhbond_nbd_refined 0.187 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.129 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.074 r_ncsr_local_group_6 0.051 r_ncsr_local_group_2 0.05 r_ncsr_local_group_5 0.05 r_ncsr_local_group_4 0.049 r_ncsr_local_group_1 0.044 r_ncsr_local_group_3 0.044 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16590 Nucleic Acid Atoms Solvent Atoms 953 Heterogen Atoms 774
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing