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Structure of beta-fructofuranosidase from Schwanniomyces occidentalis complexed with sucrose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KF3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 20% PEG 6000, 0.2 M MgCl2, and 0.1 M HEPES pH 7.0, by mixing 1 uL of protein with 0.5 uL of mother liquor. Crystals were soaked in mother liquor supplemented with 83 mM fructosyl-manitol, contaminated with sucrose. Cryoprotectant mother liquor supplemented with 25% ethylene glycol.
Crystal Properties Matthews coefficient Solvent content 2.63 53.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.903 α = 90 b = 93.201 β = 104.9 c = 116.615 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS3 S 6M KB focusing mirrors 2016-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979260 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.09 49.74 99.9 0.138 0.156 0.07 0.981 8.6 5 74544 17.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.13 99.8 0.569 0.64 0.286 0.802 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3KF3 2.09 49.74 70862 3606 99.79 0.1768 0.17495 0.21362 0.1988 RANDOM 19.547
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] 1.95 -0.55 -0.66 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.161 r_dihedral_angle_4_deg 15.199 r_dihedral_angle_3_deg 13.658 r_dihedral_angle_1_deg 7.472 r_long_range_B_refined 4.749 r_long_range_B_other 4.678 r_scangle_other 3.29 r_mcangle_it 2.214 r_mcangle_other 2.214 r_scbond_it 1.993
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.161 r_dihedral_angle_4_deg 15.199 r_dihedral_angle_3_deg 13.658 r_dihedral_angle_1_deg 7.472 r_long_range_B_refined 4.749 r_long_range_B_other 4.678 r_scangle_other 3.29 r_mcangle_it 2.214 r_mcangle_other 2.214 r_scbond_it 1.993 r_scbond_other 1.993 r_angle_refined_deg 1.459 r_angle_other_deg 1.356 r_mcbond_it 1.334 r_mcbond_other 1.334 r_chiral_restr 0.071 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8308 Nucleic Acid Atoms Solvent Atoms 794 Heterogen Atoms 248
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing