7ALL | pdb_00007all

A single sulfatase is required for metabolism of colonic mucin O-glycans and intestinal colonization by a symbiotic human gut bacterium (BT4683-S1_4)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HDH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	20 % PEG 3350, 0.2 M sodium iodide and BTP pH 8.5 25mg/ml

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.136	α = 90
b = 87.799	β = 90
c = 101.833	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 EIGER2 X 16M		2019-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.98	Diamond	I04

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	1.63	66.585	99.9	0.999	7.8	1.9		62376

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	1.63	1.66			0.795	1.4

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	1HDH	1.63	66.585	62376	3095	99.896	0.175	0.174	0.18	0.2003	0.21	22.124

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]
-1.456			-1.189		2.645

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.3
r_dihedral_angle_4_deg	18.507
r_dihedral_angle_3_deg	14.339
r_dihedral_angle_1_deg	6.977
r_lrange_it	4.733
r_lrange_other	4.665
r_scangle_it	3.921
r_scangle_other	3.92
r_scbond_it	2.555
r_scbond_other	2.554
r_mcangle_other	2.146
r_mcangle_it	2.142
r_angle_refined_deg	1.53
r_mcbond_it	1.518
r_mcbond_other	1.504
r_angle_other_deg	1.389
r_metal_ion_refined	0.251
r_nbd_refined	0.203
r_nbd_other	0.202
r_symmetry_nbd_other	0.178
r_nbtor_refined	0.172
r_symmetry_nbd_refined	0.163
r_symmetry_xyhbond_nbd_refined	0.158
r_xyhbond_nbd_refined	0.127
r_chiral_restr	0.077
r_symmetry_nbtor_other	0.075
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3991
Nucleic Acid Atoms
Solvent Atoms	309
Heterogen Atoms	31

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
BALBES	phasing