4YQP

Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	ROTATING ANODE
Source details	RIGAKU FR-E+ SUPERBRIGHT
Temperature [K]	100
Detector technology	CCD
Collection date	2010-05-27
Detector	RIGAKU SATURN 944+
Wavelength(s)	1.54
Spacegroup name	H 3 2
Unit cell lengths	94.775, 94.775, 178.306
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	39.993 - 2.601
R-factor	0.18
Rwork	0.172
R-free	0.25340
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	1p9p
RMSD bond length	0.008
RMSD bond angle	1.127
Data scaling software	HKL-2000
Phasing software	PHASER
Refinement software	PHENIX

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	50.000	50.000	2.640
High resolution limit [Å]	2.600	7.050	2.600
Rmerge	0.156	0.044	0.650
Total number of observations	93933
Number of reflections	9471
<I/σ(I)>	5.5
Completeness [%]	97.3	98.5	96.2
Redundancy	9.9	8.9	10

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	Protein solution:( 12/mg/mL in 100mM HEPES pH 7.5, 150mM NaCl, 10mM MgCl2 2mM DTT) Well solution: (20% PEG3,350 and 0.2M potassium citrate tribasic monohydrate). 4uL of S-adenosyl methionine in water were added to 100uL of protein and allowed to incubate on ice for 1 hour before protein was mixed with well at 1:1 ratio.Seeding used to improve crystals. Compound stock solutions (either 100mM or 1M stocks) were added up to a final drop concentration of 4.8% DMSO. Crystals were soaked for 4-6 hours. 20% glycerol in well solution was used as cryoprotectant for a quick dip of crystal in liquid N2.