7X87

The complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with sophotetraose observed as sophorose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7VKW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52980.1M Tris-HCl (pH 7.5), 0.2M calcium acetate, 20%(w/v) PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.1943.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 165.135α = 90
b = 71.615β = 104.894
c = 130.308γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102017-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.7947.931000.9959.43.8138455
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.791.8299.70.571.63.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7VKW1.7947.905138450680899.9690.1680.16630.200517.597
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]
0.010.02-0.011-0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.082
r_dihedral_angle_4_deg20.766
r_dihedral_angle_3_deg14.266
r_dihedral_angle_1_deg7.004
r_lrange_it4.822
r_lrange_other4.822
r_scangle_it3.625
r_scangle_other3.625
r_scbond_it2.283
r_scbond_other2.283
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.082
r_dihedral_angle_4_deg20.766
r_dihedral_angle_3_deg14.266
r_dihedral_angle_1_deg7.004
r_lrange_it4.822
r_lrange_other4.822
r_scangle_it3.625
r_scangle_other3.625
r_scbond_it2.283
r_scbond_other2.283
r_mcangle_it2.255
r_mcangle_other2.255
r_angle_refined_deg1.591
r_mcbond_it1.518
r_mcbond_other1.505
r_angle_other_deg1.381
r_symmetry_nbd_refined0.35
r_nbd_other0.3
r_nbd_refined0.208
r_nbtor_refined0.177
r_symmetry_nbd_other0.176
r_xyhbond_nbd_refined0.15
r_metal_ion_refined0.149
r_symmetry_xyhbond_nbd_refined0.119
r_symmetry_metal_ion_refined0.087
r_chiral_restr0.083
r_symmetry_nbtor_other0.078
r_symmetry_xyhbond_nbd_other0.049
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11687
Nucleic Acid Atoms
Solvent Atoms863
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing