8I2Q

Beijerinckia indica beta-fructosyltransferase variant H395R/F473Y


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6M0D 

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
1.9537.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.456α = 90
b = 82.096β = 90
c = 99.727γ = 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
12.1547.899.90.1180.0511.16.525014
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)
12.152.271000.4840.2053.76.5

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 REPLACEMENTTHROUGHOUT2.1547.8423677128699.830.171460.169690.20296RANDOM30.392
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.632
r_dihedral_angle_3_deg14.725
r_dihedral_angle_4_deg13.865
r_dihedral_angle_1_deg7.861
r_long_range_B_refined4.646
r_long_range_B_other4.59
r_scangle_other3.143
r_mcangle_other2.871
r_mcangle_it2.868
r_angle_other_deg2.345
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.632
r_dihedral_angle_3_deg14.725
r_dihedral_angle_4_deg13.865
r_dihedral_angle_1_deg7.861
r_long_range_B_refined4.646
r_long_range_B_other4.59
r_scangle_other3.143
r_mcangle_other2.871
r_mcangle_it2.868
r_angle_other_deg2.345
r_scbond_it2.03
r_scbond_other2.029
r_mcbond_it1.85
r_mcbond_other1.842
r_angle_refined_deg1.479
r_chiral_restr0.065
r_bond_other_d0.035
r_gen_planes_other0.008
r_bond_refined_d0.006
r_gen_planes_refined0.006
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 Atoms3707
Nucleic Acid Atoms
Solvent Atoms270
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing