6S3Z

Structure Of D80A-Fructofuranosidase From Xanthophyllomyces Dendrorhous Complexed With Fructose And hydroquinone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5ANN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2911.2 M Sodium Citrate tribasic dihydrate, then soaked in 20mM fructose plus 50 mM hydroquinone
Crystal Properties
Matthews coefficientSolvent content
4.0873.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.559α = 90
b = 205.949β = 90
c = 146.162γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKB mirrors2015-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979460ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.8548.761000.0690.02816.46.8192124
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)RedundancyNumber Unique Reflections (All)
11.851.881000.5870.2413.36.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT5ann1.8548.61182328968499.970.161420.160420.18035RANDOM26.764
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]
1.32-2.371.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.364
r_dihedral_angle_4_deg18.011
r_dihedral_angle_3_deg10.982
r_dihedral_angle_1_deg7.584
r_long_range_B_refined6.364
r_long_range_B_other6.337
r_scangle_other5.428
r_scbond_it3.644
r_scbond_other3.644
r_mcangle_it2.717
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.364
r_dihedral_angle_4_deg18.011
r_dihedral_angle_3_deg10.982
r_dihedral_angle_1_deg7.584
r_long_range_B_refined6.364
r_long_range_B_other6.337
r_scangle_other5.428
r_scbond_it3.644
r_scbond_other3.644
r_mcangle_it2.717
r_mcangle_other2.717
r_mcbond_other2.256
r_mcbond_it2.255
r_angle_refined_deg1.776
r_angle_other_deg1.47
r_chiral_restr0.087
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
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 AtomsNumber
Protein Atoms9588
Nucleic Acid Atoms
Solvent Atoms971
Heterogen Atoms876

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing