7OZC

Sulfated host glycan recognition by carbohydrate sulfatases of the human gut microbiota (BT3109_S1_15)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6S20 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29310 mg/ml of BT3109S1_15 with 10 mM 6S-Gal was crystallised in 30 % PEG 4000, 0.2 M ammonium acetate and sodium citrate pH 5.6.
Crystal Properties
Matthews coefficientSolvent content
1.9737.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.15α = 90
b = 91.76β = 116.63
c = 52.68γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2019-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9762DiamondI03

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
11.7547.13699.50.9978.83.544392
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)
11.751.780.4931.2

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-VALUE6S201.7547.0944366207199.3080.1850.18360.21727.325
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]
-2.1420.2420.2131.122
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.428
r_dihedral_angle_4_deg15.537
r_dihedral_angle_3_deg14.505
r_dihedral_angle_1_deg7.113
r_lrange_it4.721
r_lrange_other4.711
r_scangle_other3.704
r_scangle_it3.703
r_mcangle_it2.496
r_mcangle_other2.496
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.428
r_dihedral_angle_4_deg15.537
r_dihedral_angle_3_deg14.505
r_dihedral_angle_1_deg7.113
r_lrange_it4.721
r_lrange_other4.711
r_scangle_other3.704
r_scangle_it3.703
r_mcangle_it2.496
r_mcangle_other2.496
r_scbond_other2.417
r_scbond_it2.415
r_mcbond_it1.854
r_mcbond_other1.853
r_angle_refined_deg1.492
r_angle_other_deg1.317
r_symmetry_xyhbond_nbd_other0.567
r_symmetry_xyhbond_nbd_refined0.212
r_nbd_refined0.203
r_symmetry_nbd_other0.179
r_xyhbond_nbd_refined0.17
r_nbd_other0.167
r_nbtor_refined0.162
r_metal_ion_refined0.101
r_symmetry_nbd_refined0.094
r_symmetry_nbtor_other0.075
r_chiral_restr0.066
r_xyhbond_nbd_other0.012
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3731
Nucleic Acid Atoms
Solvent Atoms186
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing