Experiment: 9XVW

Crystal structure of mature Bacteroides fragilis toxin 2

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Crystals were grown from a crystallization solution containing 0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate pH 6.5 and 30% (w/v) PEG 8000. The protein solution was at a concentration of 20 mg/ml.

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.122	α = 90
b = 47.122	β = 90
c = 148.045	γ = 120

Symmetry
Space Group	P 31

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 PILATUS3 6M		2024-04-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97907	SSRF	BL19U1

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	2.5	41.02	99.9	0.97	6	10.1		12657			24.18

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.95	3.11	100		1.064	0.345	0.74		10.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.5	40.81	2	12657	633	99.98	0.2212	0.2185	0.2192	0.2719	0.2716	27.05

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.8335
f_angle_d	0.4067
f_chiral_restr	0.038
f_plane_restr	0.0028
f_bond_d	0.0016

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3072
Nucleic Acid Atoms
Solvent Atoms	81
Heterogen Atoms	2

Software

Software
Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing