6S2G

Structure Of D80A-Fructofuranosidase From Xanthophyllomyces Dendrorhous Complexed With Fructose And Epigallocatechin Gallate (Egcg)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291PROTEIN WAS CRYSTALLIZED FROM 1.3M SODIUM CITRATE TRIBASIC DIHYDRATE, THEN SOAKED IN 20MM FRUCTOSE PLUS 50MM EGCG
Crystal Properties
Matthews coefficientSolvent content
4.0873.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.85α = 90
b = 205.974β = 90
c = 145.17γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6MKB MIRRORS2014-07-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979489ALBAXALOC

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
12.03118.661000.080.03315.26.8145475
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)
12.032.061000.5560.233.56.8

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5ANN2.03118.6613802173491000.1670.1660.188RANDOM33.73
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]
0.55-3.152.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.764
r_dihedral_angle_4_deg16.621
r_dihedral_angle_3_deg10.782
r_dihedral_angle_1_deg6.758
r_long_range_B_refined6.001
r_long_range_B_other5.838
r_scangle_other3.732
r_scbond_it2.317
r_scbond_other2.317
r_mcangle_it2.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.764
r_dihedral_angle_4_deg16.621
r_dihedral_angle_3_deg10.782
r_dihedral_angle_1_deg6.758
r_long_range_B_refined6.001
r_long_range_B_other5.838
r_scangle_other3.732
r_scbond_it2.317
r_scbond_other2.317
r_mcangle_it2.11
r_mcangle_other2.11
r_angle_refined_deg1.534
r_mcbond_it1.403
r_mcbond_other1.403
r_angle_other_deg1.051
r_chiral_restr0.14
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.003
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 AtomsNumber
Protein Atoms9588
Nucleic Acid Atoms
Solvent Atoms955
Heterogen Atoms1142

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing