7AN1

A single sulfatase is required for metabolism of colonic mucin O-glycans and intestinal colonization by a symbiotic human gut bacterium (BT1636-S1_20)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FSU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293BT1636 (20 mg/ml) with 20 mM LacNAc crystallised in 40 % MPD and 0.2 M sodium cacodylate pH 6.5.
Crystal Properties
Matthews coefficientSolvent content
2.957.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.28α = 90
b = 87.85β = 90
c = 103.31γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2018-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9790DiamondI04

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
11.551.70999.10.99711.27107725
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)
11.51.530.6561.4

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-VALUE1FSU1.551.708107642554699.0640.1420.14110.167224.081
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]
2.057-4.7872.729
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.856
r_dihedral_angle_4_deg16.18
r_dihedral_angle_3_deg12.369
r_dihedral_angle_1_deg7.34
r_lrange_it4.469
r_lrange_other4.392
r_rigid_bond_restr4.057
r_scangle_it3.917
r_scangle_other3.917
r_mcangle_other3.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.856
r_dihedral_angle_4_deg16.18
r_dihedral_angle_3_deg12.369
r_dihedral_angle_1_deg7.34
r_lrange_it4.469
r_lrange_other4.392
r_rigid_bond_restr4.057
r_scangle_it3.917
r_scangle_other3.917
r_mcangle_other3.315
r_mcangle_it3.313
r_scbond_other3.226
r_scbond_it3.225
r_mcbond_it2.602
r_mcbond_other2.597
r_angle_refined_deg1.503
r_angle_other_deg1.4
r_nbd_refined0.21
r_symmetry_xyhbond_nbd_refined0.187
r_symmetry_nbd_refined0.185
r_symmetry_nbd_other0.183
r_nbtor_refined0.173
r_xyhbond_nbd_refined0.133
r_metal_ion_refined0.119
r_nbd_other0.095
r_chiral_restr0.081
r_symmetry_nbtor_other0.078
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3877
Nucleic Acid Atoms
Solvent Atoms384
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
BALBESphasing