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Structure of Fructofuranosidase from Purpureocilum lilacinum
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 4.6 291 0.1M sodium acetate buffer, pH 4.6 and 2M ammonium sulfate using 2:1 ratio (protein:reservoir). Cryoprotected with 20% PEG400 and flash-cooled in liquid nitrogen.
Crystal Properties Matthews coefficient Solvent content 2.35 47.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.412 α = 90 b = 111.693 β = 90 c = 219.254 γ = 90
Symmetry Space Group C 2 2 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 2024-07-27 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 2.1 46.9 98.29 0.16 0.068 0.998 14.4 12.2 73064
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 97.05 0.696 0.298 0.939 4.4 11.7
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-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 2.1 46.809 72976 3664 98.372 0.196 0.19573 0.194 0.2025 0.2312 0.2375 RANDOM 20.944
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] -0.312 0.581 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.165 r_dihedral_angle_6_deg 13.117 r_dihedral_angle_3_deg 11.334 r_dihedral_angle_1_deg 7.163 r_lrange_it 6.178 r_lrange_other 6.167 r_scangle_it 3.991 r_scangle_other 3.991 r_mcangle_it 3.278 r_mcangle_other 3.278
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.165 r_dihedral_angle_6_deg 13.117 r_dihedral_angle_3_deg 11.334 r_dihedral_angle_1_deg 7.163 r_lrange_it 6.178 r_lrange_other 6.167 r_scangle_it 3.991 r_scangle_other 3.991 r_mcangle_it 3.278 r_mcangle_other 3.278 r_scbond_it 2.561 r_scbond_other 2.561 r_mcbond_it 2.057 r_mcbond_other 2.057 r_angle_refined_deg 1.438 r_angle_other_deg 0.768 r_nbd_other 0.27 r_nbd_refined 0.232 r_symmetry_nbd_other 0.222 r_symmetry_nbd_refined 0.186 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.134 r_symmetry_nbtor_other 0.119 r_symmetry_xyhbond_nbd_refined 0.097 r_chiral_restr 0.073 r_ncsr_local_group_1 0.063 r_bond_other_d 0.016 r_gen_planes_refined 0.01 r_gen_planes_other 0.01 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8289 Nucleic Acid Atoms Solvent Atoms 514 Heterogen Atoms 347
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing