7ALL

A single sulfatase is required for metabolism of colonic mucin O-glycans and intestinal colonization by a symbiotic human gut bacterium (BT4683-S1_4)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29520 % PEG 3350, 0.2 M sodium iodide and BTP pH 8.5 25mg/ml
Crystal Properties
Matthews coefficientSolvent content
2.0740.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.136α = 90
b = 87.799β = 90
c = 101.833γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2019-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.98DiamondI04

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
11.6366.58599.90.9997.81.962376
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)
11.631.660.7951.4

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-VALUE1HDH1.6366.58562376309599.8960.1750.1740.200322.124
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]
-1.456-1.1892.645
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.3
r_dihedral_angle_4_deg18.507
r_dihedral_angle_3_deg14.339
r_dihedral_angle_1_deg6.977
r_lrange_it4.733
r_lrange_other4.665
r_scangle_it3.921
r_scangle_other3.92
r_scbond_it2.555
r_scbond_other2.554
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.3
r_dihedral_angle_4_deg18.507
r_dihedral_angle_3_deg14.339
r_dihedral_angle_1_deg6.977
r_lrange_it4.733
r_lrange_other4.665
r_scangle_it3.921
r_scangle_other3.92
r_scbond_it2.555
r_scbond_other2.554
r_mcangle_other2.146
r_mcangle_it2.142
r_angle_refined_deg1.53
r_mcbond_it1.518
r_mcbond_other1.504
r_angle_other_deg1.389
r_metal_ion_refined0.251
r_nbd_refined0.203
r_nbd_other0.202
r_symmetry_nbd_other0.178
r_nbtor_refined0.172
r_symmetry_nbd_refined0.163
r_symmetry_xyhbond_nbd_refined0.158
r_xyhbond_nbd_refined0.127
r_chiral_restr0.077
r_symmetry_nbtor_other0.075
r_bond_refined_d0.009
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 Atoms3991
Nucleic Acid Atoms
Solvent Atoms309
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
BALBESphasing