7OZC | pdb_00007ozc

Sulfated host glycan recognition by carbohydrate sulfatases of the human gut microbiota (BT3109_S1_15)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6S20

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	10 mg/ml of BT3109S1_15 with 10 mM 6S-Gal was crystallised in 30 % PEG 4000, 0.2 M ammonium acetate and sodium citrate pH 5.6.

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.15	α = 90
b = 91.76	β = 116.63
c = 52.68	γ = 90

Symmetry
Space Group	P 1 21 1

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		2019-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	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	1.75	47.136	99.5	0.997	8.8	3.5		44392

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	1.75	1.78			0.493	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	FREE R-VALUE	6S20	1.75	47.09	44366	2071	99.308	0.185	0.1836	0.19	0.217	0.22	27.325

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]
-2.142		0.242	0.213		1.122

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.428
r_dihedral_angle_4_deg	15.537
r_dihedral_angle_3_deg	14.505
r_dihedral_angle_1_deg	7.113
r_lrange_it	4.721
r_lrange_other	4.711
r_scangle_other	3.704
r_scangle_it	3.703
r_mcangle_it	2.496
r_mcangle_other	2.496
r_scbond_other	2.417
r_scbond_it	2.415
r_mcbond_it	1.854
r_mcbond_other	1.853
r_angle_refined_deg	1.492
r_angle_other_deg	1.317
r_symmetry_xyhbond_nbd_other	0.567
r_symmetry_xyhbond_nbd_refined	0.212
r_nbd_refined	0.203
r_symmetry_nbd_other	0.179
r_xyhbond_nbd_refined	0.17
r_nbd_other	0.167
r_nbtor_refined	0.162
r_metal_ion_refined	0.101
r_symmetry_nbd_refined	0.094
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.066
r_xyhbond_nbd_other	0.012
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3731
Nucleic Acid Atoms
Solvent Atoms	186
Heterogen Atoms	17

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing