6M0E

Beijerinckia indica beta-fructosyltransferase complexed with fructose


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 MgCl2, 0.1 M Na K tartrate, 0.1 M Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
1.9336.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.377α = 90
b = 81.521β = 90
c = 99.081γ = 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
11.3545.298.90.0470.0219.46.696105
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)
11.351.4297.70.4680.194.16.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6M0D1.3545.296024466398.6830.1510.14990.166315.306
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]
-0.0010.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.462
r_dihedral_angle_4_deg14.977
r_dihedral_angle_3_deg11.648
r_dihedral_angle_1_deg7.272
r_lrange_it4.316
r_lrange_other3.981
r_scangle_it2.345
r_scangle_other2.345
r_angle_other_deg2.31
r_mcangle_other1.738
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.462
r_dihedral_angle_4_deg14.977
r_dihedral_angle_3_deg11.648
r_dihedral_angle_1_deg7.272
r_lrange_it4.316
r_lrange_other3.981
r_scangle_it2.345
r_scangle_other2.345
r_angle_other_deg2.31
r_mcangle_other1.738
r_mcangle_it1.735
r_scbond_it1.499
r_scbond_other1.498
r_angle_refined_deg1.47
r_mcbond_it1.082
r_mcbond_other1.067
r_nbd_other0.232
r_symmetry_nbd_other0.207
r_nbd_refined0.196
r_nbtor_refined0.176
r_symmetry_xyhbond_nbd_refined0.139
r_xyhbond_nbd_refined0.111
r_symmetry_nbtor_other0.076
r_chiral_restr0.071
r_symmetry_nbd_refined0.063
r_bond_other_d0.036
r_gen_planes_other0.01
r_bond_refined_d0.008
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3701
Nucleic Acid Atoms
Solvent Atoms583
Heterogen Atoms63

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing