5FMD

Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with nystose


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5PROTEIN WAS CRYSTALLIZED FROM 1.25M SODIUM CITRATE TRIBASIC DIHYDRATE, THEN SOAKED IN 50MM NYSTOSE, pH 6.5
Crystal Properties
Matthews coefficientSolvent content
4.0870.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.552α = 90
b = 205.405β = 90
c = 146.362γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKB MIRRORS2014-07-16MSINGLE 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
11.78119.21000.0716.26.7215107
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)
11.781.811000.553.66.7

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 5ANN1.78119.22042491074199.970.167170.166610.17782RANDOM25.93
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]
1.32-2.220.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.247
r_dihedral_angle_4_deg16.818
r_dihedral_angle_3_deg10.231
r_dihedral_angle_1_deg6.662
r_scbond_it1.756
r_mcangle_it1.463
r_angle_refined_deg1.371
r_angle_other_deg0.976
r_mcbond_it0.931
r_mcbond_other0.931
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.247
r_dihedral_angle_4_deg16.818
r_dihedral_angle_3_deg10.231
r_dihedral_angle_1_deg6.662
r_scbond_it1.756
r_mcangle_it1.463
r_angle_refined_deg1.371
r_angle_other_deg0.976
r_mcbond_it0.931
r_mcbond_other0.931
r_chiral_restr0.079
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_it
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 Atoms1444
Heterogen Atoms911

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing