7ANB | pdb_00007anb

A single sulfatase is required for metabolism of colonic mucin O-glycans and intestinal colonization by a symbiotic human gut bacterium (BT1622-S1_20)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		BT1624

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	20 % PEG 3350, 0.2 M Sodium citrate, 25 mg/ml BT1622 and 10 mM LacNAc.

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.268	α = 90
b = 81.268	β = 90
c = 383.735	γ = 90

Symmetry
Space Group	P 43 21 2

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 XE 16M		2018-07-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9790	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	2.6	96.118	97.8	0.987	5.5	7.3		40144

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	2.6	2.71			0.344

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	BT1624	2.6	95.93	40015	1975	97.614	0.22	0.2187	0.22	0.2448	0.25	57.279

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]
0.003			0.003		-0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.258
r_dihedral_angle_4_deg	19.037
r_dihedral_angle_3_deg	15.265
r_dihedral_angle_1_deg	7.398
r_lrange_it	1.879
r_lrange_other	1.875
r_angle_refined_deg	1.319
r_angle_other_deg	1.129
r_mcangle_it	0.672
r_mcangle_other	0.672
r_scangle_it	0.572
r_scangle_other	0.572
r_mcbond_it	0.379
r_mcbond_other	0.379
r_scbond_it	0.32
r_scbond_other	0.32
r_nbd_refined	0.189
r_metal_ion_refined	0.179
r_symmetry_nbd_other	0.176
r_nbd_other	0.171
r_nbtor_refined	0.164
r_symmetry_nbd_refined	0.155
r_xyhbond_nbd_refined	0.143
r_symmetry_xyhbond_nbd_refined	0.126
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.054
r_ncsr_local_group_1	0.049
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7570
Nucleic Acid Atoms
Solvent Atoms	29
Heterogen Atoms	24

Software

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