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Structure Of D80A-Fructofuranosidase From Xanthophyllomyces Dendrorhous Complexed With Fructose And Catechol
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, HANGING DROP 291 1.2M SODIUM CITRATE TRIBASIC DIHYDRATE, THEN SOAKED IN 20MM FRUCTOSE PLUS 50MM CATECHOL
Crystal Properties Matthews coefficient Solvent content 4.08 73.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.715 α = 90 b = 204.743 β = 90 c = 147.27 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 2015-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 1.041910 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.8 119.55 100 0.086 0.036 11.8 6.7 209132
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 99.9 0.537 0.226 2.7 6.5
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 5ANN 1.8 119.55 198633 10365 100 0.164 0.164 0.172 0.182 RANDOM 25.14
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] 0.57 -2.28 1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.667 r_dihedral_angle_4_deg 16.424 r_dihedral_angle_3_deg 10.295 r_dihedral_angle_1_deg 6.682 r_long_range_B_refined 4.922 r_long_range_B_other 4.402 r_scangle_other 2.639 r_scbond_it 1.597 r_scbond_other 1.597 r_mcangle_it 1.355
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.667 r_dihedral_angle_4_deg 16.424 r_dihedral_angle_3_deg 10.295 r_dihedral_angle_1_deg 6.682 r_long_range_B_refined 4.922 r_long_range_B_other 4.402 r_scangle_other 2.639 r_scbond_it 1.597 r_scbond_other 1.597 r_mcangle_it 1.355 r_mcangle_other 1.355 r_angle_refined_deg 1.33 r_angle_other_deg 0.97 r_mcbond_it 0.86 r_mcbond_other 0.86 r_chiral_restr 0.077 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 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 9588 Nucleic Acid Atoms Solvent Atoms 1299 Heterogen Atoms 841
Software Software Software Name Purpose XDS data reduction Aimless data scaling MOLREP phasing REFMAC refinement