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Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with fructosyl-hydroxytyrosol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ANN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 Protein was crystallized from 1.3M Sodium Citrate tribasic dihydrate
Crystal Properties Matthews coefficient Solvent content 4.08 73.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.616 α = 90 b = 205.356 β = 90 c = 146.94 γ = 90
Symmetry Space Group P 21 21 2
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 KB mirrors 2016-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 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 1.91 48.98 100 0.072 0.03 0.999 19 6.8 175297
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.91 1.94
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 FOURIER SYNTHESIS THROUGHOUT 5ANN 1.91 48.98 166479 8690 99.96 0.16854 0.16782 0.1766 0.18213 0.1912 RANDOM 25.674
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] 1.23 -2.73 1.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.03 r_dihedral_angle_4_deg 17.295 r_dihedral_angle_3_deg 11.162 r_dihedral_angle_1_deg 6.718 r_long_range_B_refined 3.952 r_long_range_B_other 3.803 r_scangle_other 1.993 r_angle_refined_deg 1.413 r_scbond_it 1.131 r_scbond_other 1.131
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.03 r_dihedral_angle_4_deg 17.295 r_dihedral_angle_3_deg 11.162 r_dihedral_angle_1_deg 6.718 r_long_range_B_refined 3.952 r_long_range_B_other 3.803 r_scangle_other 1.993 r_angle_refined_deg 1.413 r_scbond_it 1.131 r_scbond_other 1.131 r_angle_other_deg 0.99 r_mcangle_it 0.98 r_mcangle_other 0.979 r_mcbond_it 0.542 r_mcbond_other 0.542 r_chiral_restr 0.086 r_bond_refined_d 0.006 r_bond_other_d 0.004 r_gen_planes_refined 0.004 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 9588 Nucleic Acid Atoms Solvent Atoms 1381 Heterogen Atoms 1019
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling