8I2R

Beijerinckia indica beta-fructosyltransferase variant H395R/F473Y in complex with fructose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6M0E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829330% (w/v) polyethylene glycol 10000, 0.2 M magnesium chloride, 0.1 M potassium sodium tartrate, 0.1 M Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
1.9536.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.542α = 90
b = 81.697β = 90
c = 99.602γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.98Photon FactoryBL-17A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
11.3647.899.70.0530.02315.66.495951
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.361.431000.480.2013.56.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.3637.8290892466999.350.16270.161740.18156RANDOM17.745
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.081
r_dihedral_angle_4_deg14.425
r_dihedral_angle_3_deg11.613
r_dihedral_angle_1_deg7.288
r_long_range_B_refined4.281
r_long_range_B_other4.038
r_scangle_other2.594
r_angle_other_deg2.302
r_mcangle_other1.935
r_mcangle_it1.932
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.081
r_dihedral_angle_4_deg14.425
r_dihedral_angle_3_deg11.613
r_dihedral_angle_1_deg7.288
r_long_range_B_refined4.281
r_long_range_B_other4.038
r_scangle_other2.594
r_angle_other_deg2.302
r_mcangle_other1.935
r_mcangle_it1.932
r_scbond_it1.666
r_scbond_other1.665
r_angle_refined_deg1.521
r_mcbond_it1.221
r_mcbond_other1.215
r_chiral_restr0.072
r_bond_other_d0.035
r_gen_planes_other0.01
r_bond_refined_d0.008
r_gen_planes_refined0.008
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 Atoms3703
Nucleic Acid Atoms
Solvent Atoms570
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing