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Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with sucrose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ANN PDB ENTRY 5ANN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 PROTEIN WAS CRYSTALLIZED FROM 1.4M SODIUM CITRATE TRIBASIC DIHYDRATE, 0.1M HEPES PH 7.5, THEN SOAKED IN 6% W/V SUCROSE
Crystal Properties Matthews coefficient Solvent content 2.07 40.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.734 α = 90 b = 205.219 β = 90 c = 146.071 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 2013-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 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 2.01 119 99 0.118 8.2 6.8 14803
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.01 2.04 98.1 0.55 2 6.9
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 PDB ENTRY 5ANN 2.01 119 140659 7326 98.73 0.16716 0.16623 0.1758 0.18473 0.1928 RANDOM 31.718
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] 2.6 -3.68 1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.042 r_dihedral_angle_4_deg 17.834 r_dihedral_angle_3_deg 10.455 r_dihedral_angle_1_deg 6.857 r_long_range_B_refined 5.927 r_long_range_B_other 5.416 r_scangle_other 3.536 r_scbond_it 2.206 r_scbond_other 2.206 r_mcangle_it 1.923
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.042 r_dihedral_angle_4_deg 17.834 r_dihedral_angle_3_deg 10.455 r_dihedral_angle_1_deg 6.857 r_long_range_B_refined 5.927 r_long_range_B_other 5.416 r_scangle_other 3.536 r_scbond_it 2.206 r_scbond_other 2.206 r_mcangle_it 1.923 r_mcangle_other 1.923 r_angle_refined_deg 1.506 r_mcbond_it 1.279 r_mcbond_other 1.279 r_angle_other_deg 1.181 r_chiral_restr 0.117 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.003 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 1511 Heterogen Atoms 913
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing