7VL3

The complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with phenyl alpha-D-glucoside


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52980.1M Tris-HCl (pH 7.5), 0.2M calcium acetate, 20%(w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.1943.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 165.124α = 90
b = 71.523β = 105.004
c = 130.151γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102017-11-27MSINGLE 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)R Merge I (Observed)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
11.8247.881000.0958.83.8131446
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.821.851000.58323.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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-VALUE1.8219.937131331652999.8990.1640.16230.203118.121
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]
-0.0020.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.231
r_dihedral_angle_4_deg20.683
r_dihedral_angle_3_deg14.442
r_dihedral_angle_1_deg7.038
r_lrange_it4.802
r_lrange_other4.801
r_scangle_it3.659
r_scangle_other3.658
r_mcangle_it2.383
r_mcangle_other2.383
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.231
r_dihedral_angle_4_deg20.683
r_dihedral_angle_3_deg14.442
r_dihedral_angle_1_deg7.038
r_lrange_it4.802
r_lrange_other4.801
r_scangle_it3.659
r_scangle_other3.658
r_mcangle_it2.383
r_mcangle_other2.383
r_scbond_it2.297
r_scbond_other2.297
r_angle_refined_deg1.591
r_mcbond_it1.587
r_mcbond_other1.586
r_angle_other_deg1.388
r_nbd_refined0.205
r_nbd_other0.2
r_nbtor_refined0.178
r_symmetry_nbd_other0.177
r_symmetry_xyhbond_nbd_refined0.153
r_xyhbond_nbd_refined0.141
r_symmetry_nbd_refined0.133
r_chiral_restr0.081
r_symmetry_nbtor_other0.078
r_metal_ion_refined0.06
r_symmetry_metal_ion_refined0.057
r_symmetry_xyhbond_nbd_other0.051
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 Atoms11666
Nucleic Acid Atoms
Solvent Atoms949
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing