7P24

Sulfated host glycan recognition by carbohydrate sulfatases of the human gut microbiota (BT3177_S1_11)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5G2V 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29320 mg/ml BT3177S1_11 with 10 mM 6S-GlcNAc crystallised in 50 % precipitant mix 1 (40% v/v PEG 500, MME; 20 % w/v PEG 20000), 0.1 M carboxcylic acids (0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.2M Sodium oxamate) and 0.1 M buffer system 3 pH 8.5 (Tris (base); BICINE).
Crystal Properties
Matthews coefficientSolvent content
2.346.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.129α = 90
b = 69.78β = 97.644
c = 96.286γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-07-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9159DiamondI04-1

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
10.9735.85691.90.9968.81.9298423
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)
10.970.990.5961.5

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-VALUE5G2V0.9735.8562983701493091.710.1240.12360.136211.374
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]
1.2810.7250.419-1.829
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.367
r_dihedral_angle_4_deg12.923
r_dihedral_angle_3_deg12.367
r_dihedral_angle_1_deg7.221
r_rigid_bond_restr3.1
r_lrange_it2.135
r_lrange_other1.753
r_angle_other_deg1.503
r_angle_refined_deg1.502
r_scangle_other1.142
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.367
r_dihedral_angle_4_deg12.923
r_dihedral_angle_3_deg12.367
r_dihedral_angle_1_deg7.221
r_rigid_bond_restr3.1
r_lrange_it2.135
r_lrange_other1.753
r_angle_other_deg1.503
r_angle_refined_deg1.502
r_scangle_other1.142
r_scangle_it1.141
r_mcangle_it1.02
r_mcangle_other1.02
r_scbond_other0.892
r_scbond_it0.891
r_mcbond_it0.791
r_mcbond_other0.788
r_nbd_refined0.247
r_nbd_other0.22
r_symmetry_nbd_refined0.199
r_symmetry_nbd_other0.181
r_nbtor_refined0.18
r_xyhbond_nbd_refined0.145
r_symmetry_xyhbond_nbd_refined0.129
r_chiral_restr0.083
r_symmetry_nbtor_other0.082
r_symmetry_xyhbond_nbd_other0.074
r_metal_ion_refined0.048
r_gen_planes_refined0.009
r_bond_refined_d0.008
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4110
Nucleic Acid Atoms
Solvent Atoms593
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing