8FC5

Crystal structure of the A2058-N6-dimethylated Thermus thermophilus 70S ribosome in complex with protein Y, hygromycin A, and azithromycin at 2.65A resolution

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 24-ID-C
Synchrotron site	APS
Beamline	24-ID-C
Temperature [K]	100
Detector technology	PIXEL
Collection date	2022-04-26
Detector	DECTRIS EIGER2 X 16M
Wavelength(s)	0.97918
Spacegroup name	P 21 21 21
Unit cell lengths	209.550, 449.770, 619.460
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	153.310 - 2.650
R-factor	0.1965
Rwork	0.194
R-free	0.23650
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6xhx
RMSD bond length	0.004
RMSD bond angle	0.873
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]	153.310	153.310	2.720
High resolution limit [Å]	2.650	11.850	2.650
Rmerge	0.203	0.052	2.148
Rmeas	0.220	0.057	2.320
Total number of observations	11403235
Number of reflections	1668125	19571	122890
<I/σ(I)>	8.1	26.38	0.98
Completeness [%]	99.8	99.1	99.9
Redundancy	6.836	6.91	6.978
CC(1/2)	0.992	0.992	0.264

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