5FK8

Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with Neo-erlose


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 5MM NEO-ERLOSE
Crystal Properties
Matthews coefficientSolvent content
4.0870.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.568α = 90
b = 205.069β = 90
c = 146.588γ = 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
11.88119.2599.30.167.46.7181368
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)
11.881.9198.60.5936.9

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 5ANN1.88119.25172233905899.130.168360.167560.18348RANDOM27.756
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]
1.4-2.551.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.429
r_dihedral_angle_4_deg17.022
r_dihedral_angle_3_deg10.362
r_dihedral_angle_1_deg6.782
r_scangle_it2.976
r_scbond_it1.833
r_mcangle_it1.545
r_angle_refined_deg1.405
r_angle_other_deg1.145
r_mcbond_it1.012
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.429
r_dihedral_angle_4_deg17.022
r_dihedral_angle_3_deg10.362
r_dihedral_angle_1_deg6.782
r_scangle_it2.976
r_scbond_it1.833
r_mcangle_it1.545
r_angle_refined_deg1.405
r_angle_other_deg1.145
r_mcbond_it1.012
r_mcbond_other1.012
r_chiral_restr0.106
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.003
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
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 Atoms1623
Heterogen Atoms889

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing