7KFF
Crystal structure of TrmD tRNA (guanine-N1)-methyltransferase from Corynebacterium diphtheriae in complex with SAH
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 19-ID |
Synchrotron site | APS |
Beamline | 19-ID |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2019-06-16 |
Detector | DECTRIS PILATUS3 X 6M |
Wavelength(s) | 0.9792 |
Spacegroup name | P 31 2 1 |
Unit cell lengths | 83.619, 83.619, 79.418 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 28.790 - 1.350 |
R-factor | 0.1315 |
Rwork | 0.131 |
R-free | 0.15380 |
Structure solution method | SAD |
RMSD bond length | 0.007 |
RMSD bond angle | 1.058 |
Data reduction software | HKL-3000 |
Data scaling software | HKL-3000 |
Phasing software | HKL-3000 |
Refinement software | PHENIX (dev_3409) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 30.000 | 1.370 |
High resolution limit [Å] | 1.350 | 1.350 |
Rmerge | 0.109 | 1.417 |
Number of reflections | 70894 | 3365 |
<I/σ(I)> | 27 | 1.71 |
Completeness [%] | 99.5 | 95.2 |
Redundancy | 12.2 | 6.1 |
CC(1/2) | 1.000 | 0.577 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 289 | 0.17 M sodium acetate, 0.085 M Tris/HCl pH 8.5, 25.5% PEG 4000, 15% glycerol |