4YPZ
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 | 2010-06-04 |
Detector | MARMOSAIC 300 mm CCD |
Wavelength(s) | 0.97856 |
Spacegroup name | H 3 2 |
Unit cell lengths | 93.773, 93.773, 179.162 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 30.083 - 1.840 |
R-factor | 0.1687 |
Rwork | 0.167 |
R-free | 0.19430 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 1p9p |
RMSD bond length | 0.006 |
RMSD bond angle | 1.003 |
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 | 1.770 |
High resolution limit [Å] | 1.710 | 3.680 | 1.710 |
Rmerge | 0.054 | 0.030 | 0.569 |
Total number of observations | 272728 | ||
Number of reflections | 33022 | ||
<I/σ(I)> | 12.1 | ||
Completeness [%] | 99.9 | 99.3 | 100 |
Redundancy | 8.3 | 7.9 | 7.8 |
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. |