7OZ8 | pdb_00007oz8

Sulfated host glycan recognition by carbohydrate sulfatases of the human gut microbiota (BT1918_S1_46)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VQR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	20 mg/ml of BT1918S1_46 with 10 mM 6S-GlcNAc was crystallised in 45 % MPD, 0.2 M CaCl2 and 0.1 M Bis-Tris pH 5.5.

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.389	α = 90
b = 56.389	β = 90
c = 279.763	γ = 120

Symmetry
Space Group	P 32 2 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		2018-08-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.979	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	1.95	48.153	100	0.99	5.8	10.3		39105

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	1.95	2			0.803

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	2vqr	1.95	48.153	39003	2032	99.936	0.189	0.1882	0.2	0.2037	0.21	29.506

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]
0.93	0.465		0.93		-3.017

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.572
r_dihedral_angle_4_deg	15.241
r_dihedral_angle_3_deg	12.875
r_dihedral_angle_1_deg	7.082
r_lrange_it	4.847
r_lrange_other	4.842
r_scangle_it	3.825
r_scangle_other	3.825
r_mcangle_it	2.895
r_mcangle_other	2.895
r_scbond_it	2.515
r_scbond_other	2.515
r_mcbond_it	2.11
r_mcbond_other	2.11
r_angle_refined_deg	1.511
r_angle_other_deg	1.321
r_nbd_refined	0.206
r_nbd_other	0.205
r_symmetry_nbd_other	0.189
r_symmetry_nbd_refined	0.189
r_nbtor_refined	0.169
r_symmetry_xyhbond_nbd_refined	0.161
r_xyhbond_nbd_refined	0.133
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.072
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3787
Nucleic Acid Atoms
Solvent Atoms	167
Heterogen Atoms	23

Software

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