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.