9D7S

Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with Api antimicrobial peptide, mRNA, A-site release factor 1, and deacylated P-site and E-site tRNAphe at 2.85A 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	2024-07-01
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.979338
Spacegroup name	P 21 21 21
Unit cell lengths	210.350, 451.320, 625.610
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	102.430 - 2.850
R-factor	0.2207
Rwork	0.218
R-free	0.26780
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6xhw
RMSD bond length	0.004
RMSD bond angle	0.807
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]	102.430	102.430	2.920
High resolution limit [Å]	2.850	12.750	2.850
Rmerge	0.295	0.038	1.743
Rmeas	0.324	0.043	1.906
Total number of observations	8078242
Number of reflections	1355591	15810	99791
<I/σ(I)>	6.42	28.46	1.02
Completeness [%]	99.1	97.4	98.9
Redundancy	5.959	5.666	6.085
CC(1/2)	0.983	0.998	0.222

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