9DFC

Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with lasso peptide lariocidin, mRNA, aminoacylated A-site Phe-tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.50A 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-1
Synchrotron site	NSLS-II
Beamline	17-ID-1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2024-03-15
Detector	DECTRIS EIGER X 9M
Wavelength(s)	1.033202
Spacegroup name	P 21 21 21
Unit cell lengths	210.100, 451.030, 622.030
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	48.620 - 2.500
R-factor	0.2185
Rwork	0.216
R-free	0.26530
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6xhw
RMSD bond length	0.008
RMSD bond angle	1.387
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]	48.620	48.620	2.560
High resolution limit [Å]	2.500	11.180	2.500
Rmerge	0.329	0.087	2.416
Rmeas	0.342	0.091	2.515
Total number of observations	27782616
Number of reflections	2006670	23545	147863
<I/σ(I)>	6.97	20.77	0.99
Completeness [%]	100.0	99.5	100
Redundancy	13.845	13.661	12.853
CC(1/2)	0.989	0.993	0.185

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