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4YQC

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

Experimental procedure
Experimental methodSINGLE WAVELENGTH
Source typeSYNCHROTRON
Source detailsAPS BEAMLINE 21-ID-G
Synchrotron siteAPS
Beamline21-ID-G
Temperature [K]100
Detector technologyCCD
Collection date2010-04-22
DetectorMARMOSAIC 300 mm CCD
Wavelength(s)0.97856
Spacegroup nameH 3 2
Unit cell lengths94.182, 94.182, 177.635
Unit cell angles90.00, 90.00, 120.00
Refinement procedure
Resolution29.124 - 1.890
R-factor0.1601
Rwork0.158
R-free0.18430
Structure solution methodMOLECULAR REPLACEMENT
Starting model (for MR)1p9p
RMSD bond length0.006
RMSD bond angle1.030
Data scaling softwareHKL-2000
Phasing softwarePHASER
Refinement softwarePHENIX
Data quality characteristics
 OverallInner shellOuter shell
Low resolution limit [Å]30.00030.0001.810
High resolution limit [Å]1.7503.7701.750
Rmerge0.0680.0330.667
Total number of observations229228
Number of reflections30783
<I/σ(I)>10.6
Completeness [%]99.699.899
Redundancy7.47.27.4
Crystallization Conditions
crystal IDmethodpHtemperaturedetails
1VAPOR DIFFUSION, SITTING DROP7.5295Protein 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.

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