6T2Q | pdb_00006t2q

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ILN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	450 mM sodium malonate pH 7.0, 24 % PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.23	61.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.918	α = 90
b = 82.918	β = 90
c = 121.31	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		2018-11-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9793	Diamond	I03

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	19.99	99.2	0.999	14	7.6		55261

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	2.05			0.472	1.2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3ILN	2	19.99	55218	2638	99.873	0.188	0.1867	0.19	0.2108	0.22	43.976

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]
-0.615			-0.615		1.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.438
r_dihedral_angle_4_deg	19.296
r_dihedral_angle_3_deg	15.078
r_dihedral_angle_1_deg	8.547
r_lrange_it	5.217
r_lrange_other	5.213
r_scangle_it	2.937
r_scangle_other	2.937
r_mcangle_it	2.169
r_mcangle_other	2.168
r_scbond_it	1.898
r_scbond_other	1.898
r_angle_refined_deg	1.626
r_mcbond_it	1.448
r_mcbond_other	1.448
r_angle_other_deg	1.29
r_symmetry_xyhbond_nbd_refined	0.57
r_symmetry_nbd_refined	0.227
r_nbd_refined	0.222
r_symmetry_nbd_other	0.189
r_nbd_other	0.181
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.141
r_metal_ion_refined	0.124
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.072
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	99
Heterogen Atoms	90

Software

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