7OQD | pdb_00007oqd

A single sulfatase is required for metabolism of colonic mucin O-glycans and intestinal colonization by a symbiotic human gut bacterium (BT1636-S1_20)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7AN1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	40 % MPD, 0.1 M sodium cacodylate with a protein concentration of 20 mg/ml and the ligand concentration (3S-LewisA) of 20 mM.

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.175	α = 90
b = 79.196	β = 90
c = 91.1	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	Bruker PHOTON III		2021-05-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	LIQUID ANODE	BRUKER METALJET	1.34

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	2.3	18.523	98.8	0.968	4.8	4		24826

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	2.3	2.38			0.76	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7AN1	2.3	18.52	24780	1269	98.588	0.241	0.2381	0.25	0.2884	0.3	19.149

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]
2.056			0.15		-2.206

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.649
r_dihedral_angle_4_deg	15.25
r_dihedral_angle_3_deg	14.436
r_dihedral_angle_1_deg	7.352
r_lrange_it	4.101
r_lrange_other	4.068
r_mcangle_other	2.044
r_mcangle_it	2.043
r_scangle_it	1.904
r_scangle_other	1.904
r_angle_refined_deg	1.533
r_mcbond_it	1.25
r_mcbond_other	1.245
r_angle_other_deg	1.176
r_scbond_it	1.172
r_scbond_other	1.172
r_symmetry_nbd_refined	0.254
r_xyhbond_nbd_refined	0.186
r_nbd_refined	0.184
r_symmetry_nbd_other	0.176
r_nbd_other	0.167
r_nbtor_refined	0.163
r_metal_ion_refined	0.115
r_symmetry_nbtor_other	0.072
r_symmetry_xyhbond_nbd_refined	0.072
r_chiral_restr	0.067
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3869
Nucleic Acid Atoms
Solvent Atoms	179
Heterogen Atoms	17

Software

Software
Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
SAINT	data scaling
PHASER	phasing