6MT9
X-ray crystal structure of Bacillus subtilis ribonucleotide reductase NrdE alpha subunit with TTP, ATP, and ADP
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | CHESS BEAMLINE F1 |
Synchrotron site | CHESS |
Beamline | F1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2018-05-05 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.9775 |
Spacegroup name | P 43 21 2 |
Unit cell lengths | 126.337, 126.337, 125.436 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 15.998 - 2.500 |
R-factor | 0.1795 |
Rwork | 0.176 |
R-free | 0.21650 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6cgm |
RMSD bond length | 0.006 |
RMSD bond angle | 0.933 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | PHENIX ((1.13_2998: ???)) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 16.000 | 2.600 |
High resolution limit [Å] | 2.500 | 2.500 |
Rmerge | 0.175 | 1.445 |
Rpim | 0.041 | 0.333 |
Number of reflections | 35371 | 3958 |
<I/σ(I)> | 14.7 | 2.2 |
Completeness [%] | 99.2 | 99.9 |
Redundancy | 17 | 17.6 |
CC(1/2) | 0.998 | 0.734 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.6 | 293 | The crystal was grown by vapor diffusion from 4.5 mg/ml holo-NrdE in 50 mM HEPES (pH 7.6), 50 mM NaCl, 5 mM MgCl2, 2 mM TCEP, and 1% glycerol, supplemented with 5 mM ATP, 0.5 mM TTP, and 1 mM GDP. The protein solution was incubated for 10 minutes with freshly added nucleotides prior to being mixed in a 1:1 hanging drop with a precipitating solution of 6% PEG 3350, 1% w/v tryptone, and 50 mM HEPES at pH 7. Crystals were cryoprotected by soaking for 5-10 seconds in well solution mixed with 8% w/v sucrose, 2% w/v glucose, 8% v/v glycerol, 8% v/v ethylene glycol and supplemented with nucleotides, TCEP, and MgCl2 adjusted to the same concentrations used in the original protein solutions. |