6FJG

Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with fructose and 4-nitrophenol


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2911.2M Sodium Citrate tribasic dihydrate
Crystal Properties
Matthews coefficientSolvent content
4.0873.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.505α = 90
b = 205.652β = 90
c = 146.512γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKB mirrors2016-05-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.9793ALBAXALOC

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
11.7384.171000.0620.0670.0260.99916.76.8234346

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 SYNTHESISTHROUGHOUT5ANN1.73119.332224751175099.950.163540.162780.17822RANDOM25.413
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]
1.1-2.111.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.176
r_dihedral_angle_4_deg17.976
r_dihedral_angle_3_deg10.509
r_dihedral_angle_1_deg6.674
r_long_range_B_refined5.049
r_long_range_B_other5.049
r_scangle_other2.93
r_scbond_it1.738
r_scbond_other1.738
r_mcangle_it1.464
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.176
r_dihedral_angle_4_deg17.976
r_dihedral_angle_3_deg10.509
r_dihedral_angle_1_deg6.674
r_long_range_B_refined5.049
r_long_range_B_other5.049
r_scangle_other2.93
r_scbond_it1.738
r_scbond_other1.738
r_mcangle_it1.464
r_mcangle_other1.464
r_angle_refined_deg1.443
r_mcbond_it0.946
r_mcbond_other0.946
r_angle_other_deg0.91
r_chiral_restr0.076
r_bond_refined_d0.007
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 Atoms1546
Heterogen Atoms955

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing