5FIX

Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with sucrose


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5PROTEIN WAS CRYSTALLIZED FROM 1.4M SODIUM CITRATE TRIBASIC DIHYDRATE, 0.1M HEPES PH 7.5, THEN SOAKED IN 6% W/V SUCROSE
Crystal Properties
Matthews coefficientSolvent content
2.0740.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.734α = 90
b = 205.219β = 90
c = 146.071γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKB MIRRORS2013-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOCALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.01119990.1188.26.814803
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.012.0498.10.5526.9

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 5ANN2.01119140659732698.730.167160.166230.18473RANDOM31.718
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]
2.6-3.681.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.042
r_dihedral_angle_4_deg17.834
r_dihedral_angle_3_deg10.455
r_dihedral_angle_1_deg6.857
r_long_range_B_refined5.927
r_long_range_B_other5.416
r_scangle_other3.536
r_scbond_it2.206
r_scbond_other2.206
r_mcangle_it1.923
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.042
r_dihedral_angle_4_deg17.834
r_dihedral_angle_3_deg10.455
r_dihedral_angle_1_deg6.857
r_long_range_B_refined5.927
r_long_range_B_other5.416
r_scangle_other3.536
r_scbond_it2.206
r_scbond_other2.206
r_mcangle_it1.923
r_mcangle_other1.923
r_angle_refined_deg1.506
r_mcbond_it1.279
r_mcbond_other1.279
r_angle_other_deg1.181
r_chiral_restr0.117
r_bond_refined_d0.008
r_gen_planes_refined0.006
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 Atoms1511
Heterogen Atoms913

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing