9DFE

Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with lasso peptide lariocidin and protein Y at 2.60A resolution

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	NSLS-II BEAMLINE 17-ID-2
Synchrotron site	NSLS-II
Beamline	17-ID-2
Temperature [K]	100
Detector technology	PIXEL
Collection date	2024-02-25
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.979338
Spacegroup name	P 21 21 21
Unit cell lengths	207.140, 444.010, 615.200
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	55.970 - 2.600
R-factor	0.2043
Rwork	0.202
R-free	0.25170
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6xhw
RMSD bond length	0.010
RMSD bond angle	1.470
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	PHASER
Refinement software	PHENIX (1.8.2)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	55.970	55.970	2.670
High resolution limit [Å]	2.600	11.630	2.600
Rmerge	0.257	0.058	1.909
Rmeas	0.283	0.064	2.104
Total number of observations	9695643
Number of reflections	1713575	20003	126218
<I/σ(I)>	6.7	23.87	0.92
Completeness [%]	100.0	98.8	100
Redundancy	5.658	5.804	5.644
CC(1/2)	0.984	0.996	0.198

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION	7.6	292	0.1-0.2 M Arginine-HCl, 0.1M Tris-HCl pH 7.6, 2.5% PEG-20K, 7-12% MPD, 0.5 mM BME