9FYZ

Crystal structure of SusA amylase 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
in silico modelAlphaFoldAF-Q8A1G0-F1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29830 mM sodium fluoride, 30 mM sodium bromide, 30 mM sodium iodide, 50 mM MES pH 6.5, 50 mM imidazole, 20% (v/v) glycerol and 10% (w/v) PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.8857.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.978α = 90
b = 105.978β = 90
c = 753.691γ = 120
Symmetry
Space GroupP 32 2 1

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)R Merge I (Observed)Rpim I (All)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
12.4358.251000.180.0411221.4212465
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)
12.432.490.32

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 REPLACEMENTTHROUGHOUT2.4358.25178136930699.950.232460.22990.28148RANDOM72.021
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]
0.020.010.02-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.307
r_long_range_B_refined13.154
r_long_range_B_other13.153
r_scangle_other10.799
r_mcangle_it10.544
r_mcangle_other10.544
r_dihedral_angle_2_deg9.924
r_scbond_it7.553
r_scbond_other7.552
r_mcbond_it7.498
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.307
r_long_range_B_refined13.154
r_long_range_B_other13.153
r_scangle_other10.799
r_mcangle_it10.544
r_mcangle_other10.544
r_dihedral_angle_2_deg9.924
r_scbond_it7.553
r_scbond_other7.552
r_mcbond_it7.498
r_mcbond_other7.498
r_dihedral_angle_1_deg6.851
r_angle_refined_deg1.445
r_angle_other_deg0.542
r_chiral_restr0.235
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 Atoms27802
Nucleic Acid Atoms
Solvent Atoms714
Heterogen Atoms291

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing