4PU3

Shewanella oneidensis MR-1 Toxin Antitoxin System HipA, HipB and its operator DNA complex (space group P212121)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DNV	PDB ENTRY 3DNV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	293	0.2 M calcium acetate hydrate, pH 7.5, 20% PEG3350, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.82	α = 90
b = 122.45	β = 90
c = 189.85	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	200	PIXEL	DECTRIS PILATUS 6M		2013-03-12	M	SINGLE WAVELENGTH
2	1	x-ray		PIXEL	DECTRIS PILATUS 2M-F		2012-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	1	EMBL/DESY, HAMBURG	X13
2	SYNCHROTRON	SLS BEAMLINE X06DA	1	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	3.39	49.39	98.93			19211	19211		1.81

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	3.39

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	PDB ENTRY 3DNV	3.39	49.381	1.99	19187	19187	960	98.81	0.259	0.256	0.3154	RANDOM

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	15.683
f_angle_d	0.8
f_chiral_restr	0.033
f_plane_restr	0.004
f_bond_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7801
Nucleic Acid Atoms	1004
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

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 R01GM157729.