8TXA
Apo Structure of (N1G37) tRNA Methyltransferase from Mycobacterium marinum
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | NSLS-II BEAMLINE 17-ID-2 |
Synchrotron site | NSLS-II |
Beamline | 17-ID-2 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2022-03-21 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 0.97935 |
Spacegroup name | P 1 |
Unit cell lengths | 56.940, 60.797, 68.072 |
Unit cell angles | 97.05, 111.99, 100.69 |
Refinement procedure
Resolution | 22.980 - 1.591 |
R-factor | 0.1894 |
Rwork | 0.188 |
R-free | 0.22370 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.010 |
RMSD bond angle | 0.940 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | PHENIX |
Refinement software | BUSTER (2.10.4) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 61.702 | 61.702 | 1.783 |
High resolution limit [Å] | 1.591 | 5.125 | 1.591 |
Rmerge | 0.069 | 0.035 | 0.653 |
Rmeas | 0.083 | 0.042 | 0.781 |
Rpim | 0.045 | 0.023 | 0.423 |
Total number of observations | 206326 | 10389 | 10236 |
Number of reflections | 64981 | 3249 | 3249 |
<I/σ(I)> | 8.67 | 21.98 | 1.72 |
Completeness [%] | 85.8 | 99.5 | 63.8 |
Completeness (spherical) [%] | 59.5 | 99.5 | 10.2 |
Completeness (ellipsoidal) [%] | 85.8 | 99.5 | 63.8 |
Redundancy | 3.18 | 3.2 | 3.15 |
CC(1/2) | 0.996 | 0.992 | 0.712 |
Anomalous completeness (spherical) | 54.8 | 93.0 | 8.3 |
Anomalous completeness | 79.1 | 93.0 | 52.1 |
Anomalous redundancy | 1.7 | 1.7 | 1.7 |
CC(ano) | 0.038 | 0.083 | -0.007 |
|DANO|/σ(DANO) | 0.8 | 0.7 | 0.7 |
Diffraction limits | Principal axes of ellipsoid fitted to diffraction cut-off surface |
1.590 Å | 0.725, 0.725, 0.725 |
1.826 Å | 0.101, 0.101, 0.101 |
2.005 Å | -0.681, -0.681, -0.681 |
Criteria used in determination of diffraction limits | local <I/sigmaI> ≥ 1.2 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | 200 ul of 0.2M MgCl2 0.1M Tris-HCl, pH 8.0; 20% (w/v) PEG 6000 |