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Structure of D188A-fructofuranosidase from Rhodotorula dairenensis in complex with raffinose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BEQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 20% PEG 3350, 0.2 M NaCl, 0.1 M BIS-TRIS pH 5.5 at 5.5 mg ml-1 concentration, 2:1 rate.
Soaking: Mother liquor solution supplemented with 30 mM raffinose. 2h
Cryocooling: Mother liquor solution supplemented with 20% glycerol
Crystal Properties Matthews coefficient Solvent content 2.23 44.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.008 α = 90 b = 114.544 β = 104.58 c = 139.165 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 PILATUS 6M KB Mirrors 2021-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979264 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 2.27 46.29 99.9 0.132 0.144 0.055 0.993 9.1 6.8 113410
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 2.27 2.31 99.9 0.689 0.744 0.401 0.866 7
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 8BEQ 2.27 46.29 107654 5731 99.84 0.2082 0.2061 0.2085 0.247 0.2461 RANDOM 47.699
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] -1.71 -0.68 3.03 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.996 r_dihedral_angle_3_deg 12.679 r_dihedral_angle_4_deg 12.398 r_dihedral_angle_1_deg 7.803 r_angle_other_deg 1.483 r_angle_refined_deg 1.445 r_chiral_restr 0.06 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_gen_planes_other 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.996 r_dihedral_angle_3_deg 12.679 r_dihedral_angle_4_deg 12.398 r_dihedral_angle_1_deg 7.803 r_angle_other_deg 1.483 r_angle_refined_deg 1.445 r_chiral_restr 0.06 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_gen_planes_other 0.006 r_bond_other_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16133 Nucleic Acid Atoms Solvent Atoms 561 Heterogen Atoms 920
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling REFMAC phasing