6T2N | pdb_00006t2n

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	5WUT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	1.6 M Tri sodium citrate pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
3.69	66.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.465	α = 90
b = 96.128	β = 90
c = 128.756	γ = 90

Symmetry
Space Group	P 21 21 21

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		2019-01-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9786	Diamond	I24

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	2.7	19.9	99.7	0.991	7.7	6.4		33933

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	2.7	2.83			0.485	1

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	FREE R-VALUE	5WUT	2.7	19.716	30371	1464	99.574	0.236	0.2334	0.24	0.2811	0.28	69.638

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]
3.102			-4.325		1.223

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.404
r_dihedral_angle_4_deg	19.783
r_dihedral_angle_3_deg	18.639
r_dihedral_angle_1_deg	10.141
r_lrange_it	7.694
r_lrange_other	7.693
r_scangle_it	5.366
r_scangle_other	5.365
r_mcangle_it	4.857
r_mcangle_other	4.857
r_scbond_it	3.305
r_scbond_other	3.304
r_mcbond_it	3.072
r_mcbond_other	3.072
r_angle_other_deg	2.456
r_angle_refined_deg	2.202
r_symmetry_nbd_refined	0.289
r_nbd_other	0.286
r_symmetry_nbd_other	0.237
r_nbd_refined	0.23
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.173
r_symmetry_nbtor_other	0.104
r_metal_ion_refined	0.095
r_chiral_restr	0.088
r_symmetry_xyhbond_nbd_other	0.071
r_bond_other_d	0.035
r_gen_planes_other	0.016
r_bond_refined_d	0.014
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4470
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
DIALS	data reduction
MOLREP	phasing
Coot	model building
BUCCANEER	model building