12DQ

Crystal structure of Thermus thermophilus 70S ribosome in complex with sparsomycin, protein Y, and P-site MTI-tripeptidyl-tRNA analog ACCA-ITM at 2.75A 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	2023-04-15
Detector	DECTRIS EIGER2 X 16M
Wavelength(s)	0.97911
Spacegroup name	P 21 21 21
Unit cell lengths	208.050, 456.260, 616.300
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	106.050 - 2.750
R-factor	0.2064
Rwork	0.203
R-free	0.26560
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	7rqa
RMSD bond length	0.009
RMSD bond angle	1.458
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]	106.050	106.050	2.820
High resolution limit [Å]	2.750	12.300	2.750
Rmerge	0.228	0.041	1.739
Rmeas	0.251	0.045	1.929
Total number of observations	7085515
Number of reflections	1318464	13096	101403
<I/σ(I)>	6.95	28.81	0.98
Completeness [%]	88.0	73.8	91.9
Redundancy	5.374	6.719	5.071
CC(1/2)	0.989	0.998	0.234

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