9KFV

Crystal structure of the methyltransferase-ribozyme 1 bound to DNA substrate (1-benzyl-adenosine derivative)

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SSRF BEAMLINE BL10U2
Synchrotron site	SSRF
Beamline	BL10U2
Temperature [K]	100
Detector technology	PIXEL
Collection date	2024-09-23
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.97918
Spacegroup name	P 41
Unit cell lengths	67.342, 67.342, 65.163
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	33.670 - 2.820
R-factor	0.199
Rwork	0.197
R-free	0.23390
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.008
RMSD bond angle	1.379
Data reduction software	autoPROC
Data scaling software	autoPROC
Phasing software	PHASER
Refinement software	PHENIX ((1.19.2_4158: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	67.340	2.970
High resolution limit [Å]	2.820	2.820
Rmerge	0.141	2.918
Rpim	0.062	1.443
Number of reflections	6850	1045
<I/σ(I)>	10.5	0.5
Completeness [%]	95.5	100
Redundancy	6.1	5
CC(1/2)	0.987	0.417

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	7.6	291	100mM NaCl, 100mM LiCl, 10mM MgCl2, 36% MPD