7OQD

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 7AN1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529340 % MPD, 0.1 M sodium cacodylate with a protein concentration of 20 mg/ml and the ligand concentration (3S-LewisA) of 20 mM.
Crystal Properties
Matthews coefficientSolvent content
2.3748.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.175α = 90
b = 79.196β = 90
c = 91.1γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELBruker PHOTON III2021-05-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1LIQUID ANODEBRUKER METALJET1.34

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
12.318.52398.80.9684.8424826
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)
12.32.380.761.6

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-VALUE7AN12.318.5224780126998.5880.2410.23810.288419.149
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]
2.0560.15-2.206
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.649
r_dihedral_angle_4_deg15.25
r_dihedral_angle_3_deg14.436
r_dihedral_angle_1_deg7.352
r_lrange_it4.101
r_lrange_other4.068
r_mcangle_other2.044
r_mcangle_it2.043
r_scangle_it1.904
r_scangle_other1.904
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.649
r_dihedral_angle_4_deg15.25
r_dihedral_angle_3_deg14.436
r_dihedral_angle_1_deg7.352
r_lrange_it4.101
r_lrange_other4.068
r_mcangle_other2.044
r_mcangle_it2.043
r_scangle_it1.904
r_scangle_other1.904
r_angle_refined_deg1.533
r_mcbond_it1.25
r_mcbond_other1.245
r_angle_other_deg1.176
r_scbond_it1.172
r_scbond_other1.172
r_symmetry_nbd_refined0.254
r_xyhbond_nbd_refined0.186
r_nbd_refined0.184
r_symmetry_nbd_other0.176
r_nbd_other0.167
r_nbtor_refined0.163
r_metal_ion_refined0.115
r_symmetry_nbtor_other0.072
r_symmetry_xyhbond_nbd_refined0.072
r_chiral_restr0.067
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3869
Nucleic Acid Atoms
Solvent Atoms179
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SAINTdata scaling
PHASERphasing