6Q2E
Crystal structure of Methanobrevibacter smithii Dph2 bound to 5'-methylthioadenosine
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 24-ID-E |
Synchrotron site | APS |
Beamline | 24-ID-E |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2018-07-05 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 0.97918 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 63.082, 81.020, 130.972 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 68.902 - 1.768 |
R-factor | 0.1823 |
Rwork | 0.180 |
R-free | 0.21930 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | Candidatus methanoperedens nitroreducens Dph2 bound to S-adenosylhomocysteine (PDB entry 6BXO) |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | PHENIX (1.14_3211) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 131.000 | 1.860 |
High resolution limit [Å] | 1.768 | 1.770 |
Rmerge | 0.033 | |
Number of reflections | 64613 | 9037 |
<I/σ(I)> | 19.3 | |
Completeness [%] | 97.6 | |
Redundancy | 3.9 | |
CC(1/2) | 0.999 | 0.800 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | 100 mM bistrispropane, pH 6.5, 16-17 % (w/v) PEG2000 monomethyl ether, 6 mM 5'-methylthioadenosine and 14 mM 2-aminobutyrate. After drops were formed by combining the sample and reservoir solutions, 300 mM NaCl was added to the reservoirs prior to sealing |