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Structure of beta-fructofuranosidase from Schwanniomyces occidentalis complexed with fructosyl-erythritol
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 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 transferred to a soaking solution containing mother liquor
and 66 mM fructosyl-erythritol for 4 hours, and subsequently to a fresh drop supplemented with 25% ethylene glycol .
Crystal Properties Matthews coefficient Solvent content 2.58 52.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.483 α = 90 b = 92.54 β = 104.71 c = 116.108 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 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 1.88 49.33 98.6 0.123 0.137 0.059 0.99 9.2 5.4 98961 17.6
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 1.88 1.91 97.9 0.63 0.7 0.3 0.773 3 5.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3KF3 1.88 49.33 94088 4859 98.42 0.15512 0.15391 0.1619 0.17853 0.1863 RANDOM 18.584
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] 1.21 -0.36 -0.09 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.722 r_dihedral_angle_3_deg 12.585 r_dihedral_angle_4_deg 11.969 r_dihedral_angle_1_deg 8.177 r_long_range_B_refined 4.836 r_long_range_B_other 4.835 r_scangle_other 3.3 r_mcangle_it 2.061 r_mcangle_other 2.06 r_scbond_it 2.037
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.722 r_dihedral_angle_3_deg 12.585 r_dihedral_angle_4_deg 11.969 r_dihedral_angle_1_deg 8.177 r_long_range_B_refined 4.836 r_long_range_B_other 4.835 r_scangle_other 3.3 r_mcangle_it 2.061 r_mcangle_other 2.06 r_scbond_it 2.037 r_scbond_other 2.036 r_angle_refined_deg 1.45 r_angle_other_deg 1.319 r_mcbond_it 1.303 r_mcbond_other 1.303 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 849 Heterogen Atoms 226
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing