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. |