Experiment: 4ATO

New insights into the mechanism of bacterial Type III toxin-antitoxin systems: selective toxin inhibition by a non-coding RNA pseudoknot

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4		PRECIPITANT CONTAINS 0.2 M AMMONIUM PHOSPHATE, 0.1 M TRIS-HCL PH 8.5, 50% MPD. CRYSTALLIZATION WITH A SITTING DROP, VAPOUR DIFFUSION METHOD.

Crystal Properties
Matthews coefficient	Solvent content
2.68	59.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.1	α = 90
b = 127.1	β = 90
c = 37.735	γ = 120

Symmetry
Space Group	P 6

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315	MIRRORS	2010-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02		Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.11	28	100	0.05	13.6	11		34618		3	40.36

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.11	2.23	99.9		0.55	4.6	11.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	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	PDB ENTRY 2XDB	2.2	27.95	1.42	34618	1713	99.94	0.1618	0.1602	0.1593	0.1917	0.1488	46.96

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]
1.0311			1.0311		-2.0622

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.693
f_angle_d	1.083
f_chiral_restr	0.082
f_bond_d	0.006
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1382
Nucleic Acid Atoms	726
Solvent Atoms	222
Heterogen Atoms	8

Software

Software
Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing