7P24 | pdb_00007p24

Sulfated host glycan recognition by carbohydrate sulfatases of the human gut microbiota (BT3177_S1_11)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5G2V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	20 mg/ml BT3177S1_11 with 10 mM 6S-GlcNAc crystallised in 50 % precipitant mix 1 (40% v/v PEG 500, MME; 20 % w/v PEG 20000), 0.1 M carboxcylic acids (0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.2M Sodium oxamate) and 0.1 M buffer system 3 pH 8.5 (Tris (base); BICINE).

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.129	α = 90
b = 69.78	β = 97.644
c = 96.286	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 PILATUS 6M-F		2018-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9159	Diamond	I04-1

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	0.97	35.856	91.9	0.996	8.8	1.9		298423

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	0.97	0.99			0.596	1.5

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	5G2V	0.97	35.856	298370	14930	91.71	0.124	0.1236	0.12	0.1362	0.14	11.374

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]
1.281		0.725	0.419		-1.829

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.367
r_dihedral_angle_4_deg	12.923
r_dihedral_angle_3_deg	12.367
r_dihedral_angle_1_deg	7.221
r_rigid_bond_restr	3.1
r_lrange_it	2.135
r_lrange_other	1.753
r_angle_other_deg	1.503
r_angle_refined_deg	1.502
r_scangle_other	1.142
r_scangle_it	1.141
r_mcangle_it	1.02
r_mcangle_other	1.02
r_scbond_other	0.892
r_scbond_it	0.891
r_mcbond_it	0.791
r_mcbond_other	0.788
r_nbd_refined	0.247
r_nbd_other	0.22
r_symmetry_nbd_refined	0.199
r_symmetry_nbd_other	0.181
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.145
r_symmetry_xyhbond_nbd_refined	0.129
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.082
r_symmetry_xyhbond_nbd_other	0.074
r_metal_ion_refined	0.048
r_gen_planes_refined	0.009
r_bond_refined_d	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4110
Nucleic Acid Atoms
Solvent Atoms	593
Heterogen Atoms	39

Software

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