6FJE

Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with fructose and glucose


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2911.1 M Sodium Citrate tribasic dihydrate
Crystal Properties
Matthews coefficientSolvent content
4.0873.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.834α = 90
b = 205.626β = 90
c = 146.306γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-03-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9762DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.8529.6999.90.0540.0580.0220.99921.16.7192473
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.8899.90.5410.5850.2210.9533.96.9

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 SYNTHESISTHROUGHOUT5ann1.85119.21182665969399.840.169390.168340.1893RANDOM30.787
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]
1.77-3.161.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.936
r_dihedral_angle_4_deg17.618
r_dihedral_angle_3_deg10.913
r_dihedral_angle_1_deg6.674
r_long_range_B_refined4.551
r_long_range_B_other4.551
r_scangle_other3.316
r_scbond_it2.04
r_scbond_other2.039
r_mcangle_it1.807
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.936
r_dihedral_angle_4_deg17.618
r_dihedral_angle_3_deg10.913
r_dihedral_angle_1_deg6.674
r_long_range_B_refined4.551
r_long_range_B_other4.551
r_scangle_other3.316
r_scbond_it2.04
r_scbond_other2.039
r_mcangle_it1.807
r_mcangle_other1.807
r_angle_refined_deg1.453
r_mcbond_it1.291
r_mcbond_other1.291
r_angle_other_deg0.921
r_chiral_restr0.078
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms1203
Heterogen Atoms987

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing