5FMB

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5PROTEIN WAS CRYSTALLIZED FROM 1.2M SODIUM CITRATE TRIBASIC DIHYDRATE, 0.1M HEPES PH 7.5
Crystal Properties
Matthews coefficientSolvent content
4.0870.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.661α = 90
b = 205.071β = 90
c = 146.256γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2014-01-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)PETRA III, EMBL c/o DESYP13 (MX1)

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
11.91119.071000.0710.16.8174276
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)
11.911.941000.482.17

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 5ANN1.91119.07165540863399.930.170450.16970.18472RANDOM27.272
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]
1.76-2.81.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.294
r_dihedral_angle_4_deg18.353
r_dihedral_angle_3_deg10.442
r_dihedral_angle_1_deg6.79
r_scbond_it1.813
r_mcangle_it1.554
r_angle_refined_deg1.45
r_angle_other_deg1.174
r_mcbond_it1.017
r_mcbond_other1.016
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.294
r_dihedral_angle_4_deg18.353
r_dihedral_angle_3_deg10.442
r_dihedral_angle_1_deg6.79
r_scbond_it1.813
r_mcangle_it1.554
r_angle_refined_deg1.45
r_angle_other_deg1.174
r_mcbond_it1.017
r_mcbond_other1.016
r_chiral_restr0.117
r_bond_refined_d0.007
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_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 Atoms1488
Heterogen Atoms875

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing