7OZ9

Sulfated host glycan recognition by carbohydrate sulfatases of the human gut microbiota (BT3057-S1_16)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7AN1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29535 mg/ml BT3057S1_16 with 10 mM 4S-GalNAc was crystallised in 20 % PEG 3350 and 0.2 M sodium nitrate
Crystal Properties
Matthews coefficientSolvent content
2.4549.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.17α = 90
b = 90.755β = 98.55
c = 94.169γ = 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
11.90765.5299.60.9928.81.985409
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)
11.911.940.392.2

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-VALUE7AN11.90765.5285408409799.5940.1870.18490.223323.895
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]
0.256-0.0040.587-0.805
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.528
r_dihedral_angle_4_deg14.651
r_dihedral_angle_3_deg14.12
r_dihedral_angle_1_deg7.14
r_lrange_it4.169
r_lrange_other4.13
r_scangle_it2.996
r_scangle_other2.996
r_mcangle_it2.35
r_mcangle_other2.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.528
r_dihedral_angle_4_deg14.651
r_dihedral_angle_3_deg14.12
r_dihedral_angle_1_deg7.14
r_lrange_it4.169
r_lrange_other4.13
r_scangle_it2.996
r_scangle_other2.996
r_mcangle_it2.35
r_mcangle_other2.35
r_scbond_it1.938
r_scbond_other1.938
r_mcbond_it1.622
r_mcbond_other1.621
r_angle_refined_deg1.478
r_angle_other_deg1.281
r_nbd_refined0.195
r_symmetry_nbd_other0.178
r_nbtor_refined0.163
r_xyhbond_nbd_refined0.157
r_metal_ion_refined0.145
r_nbd_other0.142
r_symmetry_nbd_refined0.114
r_symmetry_xyhbond_nbd_other0.093
r_symmetry_xyhbond_nbd_refined0.087
r_symmetry_nbtor_other0.075
r_chiral_restr0.069
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7540
Nucleic Acid Atoms
Solvent Atoms405
Heterogen Atoms78

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing