5D9F

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

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 21-ID-G
Synchrotron site	APS
Beamline	21-ID-G
Temperature [K]	100
Detector technology	CCD
Collection date	2010-04-27
Detector	MARMOSAIC 300 mm CCD
Wavelength(s)	0.97856
Spacegroup name	H 3 2
Unit cell lengths	94.784, 94.784, 178.164
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	47.392 - 1.910
R-factor	0.191
Rwork	0.188
R-free	0.21950
RMSD bond length	0.006
RMSD bond angle	1.064
Data scaling software	SCALA (3.2.5)
Phasing software	PHASER
Refinement software	PHENIX ((phenix.refine: 1.8_1065))

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	74.553	74.536	2.010
High resolution limit [Å]	1.910	6.040	1.910
Rmerge	0.093	0.026	0.916
Total number of observations	147262	4940	20016
Number of reflections	23203
<I/σ(I)>	13	39.9	1.8
Completeness [%]	96.3	99	90.5
Redundancy	6.3	6	6.3

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