7AB3

Crystal structure of the Escherichia coli toxin-antitoxin system HipBST (HipT S57A)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4PU4	Emsemble model from 4PU4, 2WIU, 3TPT, 4PU3 and 4PU5
experimental model	PDB	2WIU	Emsemble model from 4PU4, 2WIU, 3TPT, 4PU3 and 4PU5
experimental model	PDB	3TPT	Emsemble model from 4PU4, 2WIU, 3TPT, 4PU3 and 4PU5
experimental model	PDB	4PU3	Emsemble model from 4PU4, 2WIU, 3TPT, 4PU3 and 4PU5
experimental model	PDB	4PU5	Emsemble model from 4PU4, 2WIU, 3TPT, 4PU3 and 4PU5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	293.15	0.1M BICINE, 8% MPD

Crystal Properties
Matthews coefficient	Solvent content
3.71	66.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 281.68	α = 90
b = 106.07	β = 90.648
c = 57.56	γ = 90

Symmetry
Space Group	C 1 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 EIGER X 16M		2018-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.97625	PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.4	49.751	99.9	0.258	0.271	0.996	10.29	9.466		66119			68.91

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.46	99.3		1.984	2.288	0.359	0.67	3.935

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Emsemble model from 4PU4, 2WIU, 3TPT, 4PU3 and 4PU5	2.4	49.75	66119	3364	99.9	0.2013	0.1994	0.2365	RANDOM	88.87

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]
-11.9926		-4.2848	6.6085		5.3841

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	19.64
t_omega_torsion	2.74
t_angle_deg	0.97
t_bond_d	0.008
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8150
Nucleic Acid Atoms
Solvent Atoms	474
Heterogen Atoms

Software

Software
Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.