6T2P

Prominent members of the human gut microbiota express endo-acting O-glycanases to initiate mucin breakdown

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	450 mM sodium malonate pH 7.0, 24% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
3.23	61.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.724	α = 90
b = 82.724	β = 90
c = 121.682	γ = 90

Symmetry
Space Group	P 41

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2018-09-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9159	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.1	82.72	99.7	0.996	8.7	6.8		47588

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.16			0.557	1.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3ILN	2.1	82.72	47526	2369	99.619	0.187	0.1856	0.2109	36.817

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]
-0.251			-0.251		0.502

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.913
r_dihedral_angle_4_deg	16.089
r_dihedral_angle_3_deg	15.394
r_dihedral_angle_1_deg	8.712
r_lrange_it	4.295
r_lrange_other	4.29
r_scangle_it	2.659
r_scangle_other	2.659
r_mcangle_it	1.878
r_mcangle_other	1.878
r_scbond_it	1.681
r_scbond_other	1.681
r_angle_refined_deg	1.589
r_angle_other_deg	1.287
r_mcbond_it	1.202
r_mcbond_other	1.2
r_symmetry_xyhbond_nbd_refined	0.389
r_symmetry_nbd_refined	0.224
r_nbd_other	0.203
r_nbd_refined	0.192
r_symmetry_nbd_other	0.179
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.149
r_metal_ion_refined	0.102
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.067
r_symmetry_xyhbond_nbd_other	0.049
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3919
Nucleic Acid Atoms
Solvent Atoms	142
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
xia2	data reduction
PHASER	phasing
Coot	model building
Aimless	data scaling