6S82

Structure Of D80A-Fructofuranosidase From Xanthophyllomyces Dendrorhous Complexed With Tris-buffer molecule And hydroquinone


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2911.3 M Sodium Citrate tribasic dihydrate, 0.1M TRIS-HCl pH 8.5, then soaked in hidroquinone
Crystal Properties
Matthews coefficientSolvent content
4.1270.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.579α = 90
b = 205.623β = 90
c = 145.369γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKB mirrors2016-02-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979490ALBAXALOC

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
11.8583.941000.0790.03214.56.8190741
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)
11.851.880.5590.2272.9

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 SYNTHESISTHROUGHOUT5ann1.8583.94181015961999.920.15520.15410.1753RANDOM26.471
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]
0.97-2.661.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.939
r_dihedral_angle_4_deg18.018
r_dihedral_angle_3_deg11.136
r_dihedral_angle_1_deg7.574
r_angle_refined_deg1.755
r_angle_other_deg1.482
r_chiral_restr0.086
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.939
r_dihedral_angle_4_deg18.018
r_dihedral_angle_3_deg11.136
r_dihedral_angle_1_deg7.574
r_angle_refined_deg1.755
r_angle_other_deg1.482
r_chiral_restr0.086
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9588
Nucleic Acid Atoms
Solvent Atoms1348
Heterogen Atoms953

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction