☰ Navigation Tabs
Structure of D81A-Fructofuranosidase from Purpureocilum lilacinum in complex with fructose
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 6.5 291 2M ammonium sulfate, 0.1M MES sodium salt pH 6.5, and 0.2M sodium chloride solution using 2:1 ratio (protein:reservoir). Cryoprotected with 20% glycerol and flash-cooled in liquid nitrogen.
Crystal Properties Matthews coefficient Solvent content 2.75 55.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.175 α = 90 b = 141.777 β = 90 c = 253.741 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 2024-12-13 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 2.4 48.805 99.7 0.153 0.063 0.998 18.2 13.3 112459
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 2.4 2.44 0.463 0.748 2.4
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.4 48.805 112036 5644 99.682 0.201 0.1991 0.2286 0.1972 41.938
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] -0.007 0.22 -0.212
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.705 r_dihedral_angle_3_deg 11.121 r_dihedral_angle_2_deg 8.013 r_lrange_other 7.905 r_lrange_it 7.902 r_dihedral_angle_1_deg 7.331 r_scangle_other 5.602 r_scangle_it 5.601 r_mcangle_it 5.319 r_mcangle_other 5.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.705 r_dihedral_angle_3_deg 11.121 r_dihedral_angle_2_deg 8.013 r_lrange_other 7.905 r_lrange_it 7.902 r_dihedral_angle_1_deg 7.331 r_scangle_other 5.602 r_scangle_it 5.601 r_mcangle_it 5.319 r_mcangle_other 5.319 r_scbond_it 3.617 r_scbond_other 3.617 r_mcbond_it 3.494 r_mcbond_other 3.494 r_angle_refined_deg 1.315 r_angle_other_deg 0.499 r_symmetry_xyhbond_nbd_refined 0.29 r_nbd_other 0.272 r_symmetry_nbd_refined 0.252 r_symmetry_nbd_other 0.211 r_nbd_refined 0.185 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.128 r_symmetry_nbtor_other 0.085 r_symmetry_xyhbond_nbd_other 0.085 r_chiral_restr 0.067 r_ncsr_local_group_1 0.053 r_ncsr_local_group_2 0.052 r_ncsr_local_group_5 0.052 r_ncsr_local_group_4 0.05 r_ncsr_local_group_3 0.048 r_ncsr_local_group_6 0.048 r_bond_refined_d 0.006 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 16609 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms 722
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing