7OZE

Sulfated host glycan recognition by carbohydrate sulfatases of the human gut microbiota (BT1624-S1_15)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29320 mg/ml BT1624-S1_15 with 10 mM 6S-GalNAc crystallised in 20 % PEG 6000, 0.2 M ammonium chloride and 0.1 M sodium acetate pH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.3247.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.401α = 90
b = 124.715β = 95.321
c = 97.137γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2018-07-18MSINGLE 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
12.750.541000.92733.756316
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)
12.72.780.6621.4

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-VALUE6S202.750.556197274199.7090.230.22870.263516.837
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]
-1.1341.092.044-1.094
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.437
r_dihedral_angle_3_deg17.453
r_dihedral_angle_4_deg16.396
r_dihedral_angle_1_deg6.778
r_lrange_it2.756
r_lrange_other2.754
r_angle_refined_deg1.343
r_mcangle_it1.247
r_mcangle_other1.247
r_scangle_it1.147
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.437
r_dihedral_angle_3_deg17.453
r_dihedral_angle_4_deg16.396
r_dihedral_angle_1_deg6.778
r_lrange_it2.756
r_lrange_other2.754
r_angle_refined_deg1.343
r_mcangle_it1.247
r_mcangle_other1.247
r_scangle_it1.147
r_scangle_other1.146
r_angle_other_deg1.138
r_mcbond_it0.712
r_mcbond_other0.712
r_scbond_it0.647
r_scbond_other0.647
r_symmetry_xyhbond_nbd_refined0.24
r_nbd_other0.222
r_metal_ion_refined0.199
r_nbd_refined0.185
r_symmetry_nbd_other0.181
r_symmetry_nbd_refined0.18
r_nbtor_refined0.154
r_xyhbond_nbd_refined0.151
r_symmetry_nbtor_other0.073
r_symmetry_xyhbond_nbd_other0.052
r_chiral_restr0.051
r_ncsr_local_group_40.051
r_ncsr_local_group_60.051
r_ncsr_local_group_20.05
r_ncsr_local_group_50.047
r_ncsr_local_group_10.045
r_ncsr_local_group_30.044
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14891
Nucleic Acid Atoms
Solvent Atoms267
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing