9S1D

Crystal structure of the methyltransferase ribozyme 1 with two 2'O-methylation (MTR1m2)

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	PETRA III, DESY BEAMLINE P11
Synchrotron site	PETRA III, DESY
Beamline	P11
Temperature [K]	100
Detector technology	PIXEL
Collection date	2021-06-06
Detector	DECTRIS EIGER2 X 16M
Wavelength(s)	1.0332
Spacegroup name	P 41 21 2
Unit cell lengths	71.323, 71.323, 83.512
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	43.170 - 2.600
R-factor	0.2216
Rwork	0.220
R-free	0.25100
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.005
RMSD bond angle	0.940
Data reduction software	XDS (June 30 2024)
Data scaling software	XDS
Phasing software	PHASER (2.8.3)
Refinement software	PHENIX (1.21.2_5419)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	43.170	2.720
High resolution limit [Å]	2.600	2.600
Rmerge	0.044	2.017
Rmeas	0.045	2.039
Rpim	0.010	0.396
Number of reflections	7084	837
<I/σ(I)>	42.9	2
Completeness [%]	100.0	100
Redundancy	25.3	27
CC(1/2)	1.000	0.583

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293.15	200 uM RNA in a ratio of A:B:C=1:1:1 in 10 mM HEPES pH7.5, 50 mM potassium chloride, 5 mM magnesium chloride and 240 uM of O6-methylguanine Crystallization cocktail: 100 mM NaCl, 100 mM LiCl, 10 mM MgCl2, 50 mM MES pH 6.4-6.7, 36-42% MPD