7P26

Sulfated host glycan recognition by carbohydrate sulfatases of the human gut microbiota (BT4631_S1_15)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7OZE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29580 mg/ml BT4631 with 10 mM 6S-Gal was crystallised in 20 % PEG 10K and 0.1 M Bicine pH8.5.
Crystal Properties
Matthews coefficientSolvent content
2.8156.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.924α = 90
b = 109.572β = 90
c = 117.531γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-09-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.9786SOLEILPROXIMA 1

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
11.35109.5798.80.99925.412.4140145
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)
11.351.370.9554.5

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-VALUE7OZE1.3580.274140055720698.6120.1240.12330.139114.129
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]
0.928-0.247-0.681
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.774
r_dihedral_angle_4_deg20.393
r_dihedral_angle_3_deg12.543
r_dihedral_angle_1_deg6.869
r_lrange_it2.719
r_lrange_other2.213
r_scangle_it1.639
r_scangle_other1.639
r_angle_refined_deg1.482
r_angle_other_deg1.474
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.774
r_dihedral_angle_4_deg20.393
r_dihedral_angle_3_deg12.543
r_dihedral_angle_1_deg6.869
r_lrange_it2.719
r_lrange_other2.213
r_scangle_it1.639
r_scangle_other1.639
r_angle_refined_deg1.482
r_angle_other_deg1.474
r_scbond_it1.374
r_scbond_other1.374
r_rigid_bond_restr1.202
r_mcangle_it1.176
r_mcangle_other1.175
r_mcbond_it0.981
r_mcbond_other0.931
r_symmetry_nbd_refined0.428
r_nbd_other0.302
r_nbd_refined0.238
r_symmetry_xyhbond_nbd_refined0.19
r_symmetry_nbd_other0.182
r_nbtor_refined0.17
r_xyhbond_nbd_refined0.139
r_metal_ion_refined0.111
r_symmetry_nbtor_other0.079
r_chiral_restr0.078
r_symmetry_xyhbond_nbd_other0.014
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3780
Nucleic Acid Atoms
Solvent Atoms599
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing