6S2H

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2911.2M SODIUM CITRATE TRIBASIC DIHYDRATE, THEN SOAKED IN 20MM FRUCTOSE PLUS 50MM CATECHOL
Crystal Properties
Matthews coefficientSolvent content
4.0873.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.715α = 90
b = 204.743β = 90
c = 147.27γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6MKB MIRRORS2015-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC1.041910ALBAXALOC

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
11.8119.551000.0860.03611.86.7209132
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)
11.81.8399.90.5370.2262.76.5

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5ANN1.8119.55198633103651000.1640.1640.172RANDOM25.14
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]
0.57-2.281.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.667
r_dihedral_angle_4_deg16.424
r_dihedral_angle_3_deg10.295
r_dihedral_angle_1_deg6.682
r_long_range_B_refined4.922
r_long_range_B_other4.402
r_scangle_other2.639
r_scbond_it1.597
r_scbond_other1.597
r_mcangle_it1.355
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.667
r_dihedral_angle_4_deg16.424
r_dihedral_angle_3_deg10.295
r_dihedral_angle_1_deg6.682
r_long_range_B_refined4.922
r_long_range_B_other4.402
r_scangle_other2.639
r_scbond_it1.597
r_scbond_other1.597
r_mcangle_it1.355
r_mcangle_other1.355
r_angle_refined_deg1.33
r_angle_other_deg0.97
r_mcbond_it0.86
r_mcbond_other0.86
r_chiral_restr0.077
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
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 AtomsNumber
Protein Atoms9588
Nucleic Acid Atoms
Solvent Atoms1299
Heterogen Atoms841

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement