4YQ2
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-F |
Synchrotron site | APS |
Beamline | 21-ID-F |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2009-11-04 |
Detector | MARMOSAIC 300 mm CCD |
Wavelength(s) | 0.97872 |
Spacegroup name | H 3 2 |
Unit cell lengths | 98.532, 98.532, 176.274 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 39.155 - 2.650 |
R-factor | 0.1816 |
Rwork | 0.176 |
R-free | 0.23290 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 1p9p |
RMSD bond length | 0.009 |
RMSD bond angle | 1.101 |
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 | 2.740 |
High resolution limit [Å] | 2.650 | 5.710 | 2.650 |
Rmerge | 0.111 | 0.037 | 0.618 |
Total number of observations | 71376 | ||
Number of reflections | 9843 | ||
<I/σ(I)> | 8.2 | ||
Completeness [%] | 100.0 | 99.8 | 100 |
Redundancy | 7.3 | 6.8 | 7.1 |
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. |