9FZ0

Crystal structure of SusG from Bacteroides thetaiotaomicron covalently bound to alpha-1,6 branched pseudo-trisaccharide activity-based probe


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6BS6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52980.1 M Carboxylic acids (Na-Formate; NH 4-Acetate; Na 3 -Citrate; NaK-Tartrate (racemic); Na-Oxamate), 0.1 M Buffer System 1 (Imidazole; MES (acid)) pH 6.5, 50 % v/v Precipitant Mix 1 (40% v/v PEG 500* MME; 20 % w/v PEG 20000)
Crystal Properties
Matthews coefficientSolvent content
3.3663.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.293α = 90
b = 127.293β = 90
c = 129.184γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2023-01-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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
12.6564.591000.9955.814.159811
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)
12.652.720.418

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 REPLACEMENTTHROUGHOUT2.6563.6556734300699.870.208870.205770.26945RANDOM73.834
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]
-3.76-3.767.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.854
r_long_range_B_refined13.291
r_long_range_B_other13.29
r_mcangle_it10.513
r_mcangle_other10.512
r_scangle_other10.255
r_mcbond_it7.155
r_dihedral_angle_1_deg7.146
r_mcbond_other7.137
r_dihedral_angle_2_deg7.029
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.854
r_long_range_B_refined13.291
r_long_range_B_other13.29
r_mcangle_it10.513
r_mcangle_other10.512
r_scangle_other10.255
r_mcbond_it7.155
r_dihedral_angle_1_deg7.146
r_mcbond_other7.137
r_dihedral_angle_2_deg7.029
r_scbond_it6.938
r_scbond_other6.917
r_angle_refined_deg1.524
r_angle_other_deg0.568
r_chiral_restr0.217
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms10067
Nucleic Acid Atoms
Solvent Atoms185
Heterogen Atoms140

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing