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Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with fructose and 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 = 74.86 α = 90 b = 206.124 β = 90 c = 145.529 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 PSI PILATUS 6M KB Mirrors 2016-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97949 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 84.11 100 0.058 18.7 6.8 247009
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 1.7 1.73
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 1.7 118.88 234410 12454 100 0.177 0.177 0.1871 0.189 0.1988 RANDOM 23.95
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] 1.14 -2.36 1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.089 r_dihedral_angle_4_deg 16.056 r_dihedral_angle_3_deg 10.456 r_dihedral_angle_1_deg 6.674 r_long_range_B_refined 4.02 r_long_range_B_other 3.856 r_scangle_other 1.423 r_angle_refined_deg 1.344 r_angle_other_deg 1.17 r_mcangle_it 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.089 r_dihedral_angle_4_deg 16.056 r_dihedral_angle_3_deg 10.456 r_dihedral_angle_1_deg 6.674 r_long_range_B_refined 4.02 r_long_range_B_other 3.856 r_scangle_other 1.423 r_angle_refined_deg 1.344 r_angle_other_deg 1.17 r_mcangle_it 0.84 r_mcangle_other 0.84 r_scbond_it 0.778 r_scbond_other 0.778 r_mcbond_it 0.459 r_mcbond_other 0.459 r_chiral_restr 0.069 r_bond_other_d 0.008 r_bond_refined_d 0.006 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 1304 Heterogen Atoms 1425
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling