9DFD

Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with lasso peptide lariocidin B, mRNA, aminoacylated A-site Phe-tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe 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-1
Synchrotron site	NSLS-II
Beamline	17-ID-1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2024-06-25
Detector	DECTRIS EIGER X 9M
Wavelength(s)	1.033210
Spacegroup name	P 21 21 21
Unit cell lengths	210.290, 450.050, 626.340
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	365.480 - 2.600
R-factor	0.2175
Rwork	0.215
R-free	0.26580
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6xhw
RMSD bond length	0.008
RMSD bond angle	1.366
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]	365.480	365.480	2.670
High resolution limit [Å]	2.600	11.630	2.600
Rmerge	0.263	0.039	2.140
Rmeas	0.284	0.043	2.310
Total number of observations	12513545
Number of reflections	1791810	20946	130477
<I/σ(I)>	7.44	29.67	0.95
Completeness [%]	99.8	98.9	98.7
Redundancy	6.984	6.801	6.943
CC(1/2)	0.987	0.998	0.160

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