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 |