5FMC

Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with fructose and BIS-TRIS propane buffer


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5PROTEIN WAS CRYSTALLIZED FROM 1.3M SODIUM CITRATE TRIBASIC DIHYDRATE, 0.1M BIS-TRIS PROPANE PH 7.5
Crystal Properties
Matthews coefficientSolvent content
4.0873.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.432α = 90
b = 204.74β = 90
c = 145.56γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2014-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
11.84118.6399.90.067.44.5192642
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)
11.841.8799.90.341.94.6

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 REPLACEMENTTHROUGHOUT5ANN1.84118.63182944959699.80.164260.163480.17907RANDOM25.2
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]
0.95-3.012.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.669
r_dihedral_angle_4_deg17.575
r_dihedral_angle_3_deg10.144
r_dihedral_angle_1_deg6.757
r_scbond_it1.789
r_mcangle_it1.415
r_angle_refined_deg1.413
r_angle_other_deg1.081
r_mcbond_it0.898
r_mcbond_other0.898
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.669
r_dihedral_angle_4_deg17.575
r_dihedral_angle_3_deg10.144
r_dihedral_angle_1_deg6.757
r_scbond_it1.789
r_mcangle_it1.415
r_angle_refined_deg1.413
r_angle_other_deg1.081
r_mcbond_it0.898
r_mcbond_other0.898
r_chiral_restr0.109
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 Atoms1492
Heterogen Atoms897

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing