4YPW

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	2010-06-16
Detector	MAR CCD 165 mm
Wavelength(s)	1
Spacegroup name	H 3 2
Unit cell lengths	92.892, 92.892, 178.097
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	39.235 - 2.311
R-factor	0.1974
Rwork	0.192
R-free	0.24770
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	1p9p
RMSD bond length	0.002
RMSD bond angle	0.560
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	2.380
High resolution limit [Å]	2.300	4.950	2.300
Rmerge	0.054	0.035	0.209
Total number of observations	94715
Number of reflections	10317
<I/σ(I)>	17
Completeness [%]	76.8	99.9	18.3
Redundancy	9.2	10.2	3.5

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.