8DCB

RNA ligase RtcB from Pyrococcus horikoshii in complex with Ni2+ and GTP

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 24-ID-C
Synchrotron site	APS
Beamline	24-ID-C
Temperature [K]	100
Detector technology	PIXEL
Collection date	2021-10-31
Detector	DECTRIS EIGER2 X 16M
Wavelength(s)	1.4857
Spacegroup name	P 21 21 21
Unit cell lengths	81.241, 137.492, 149.559
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	49.520 - 2.600
R-factor	0.1723
Rwork	0.170
R-free	0.20860
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	4isz
RMSD bond length	0.008
RMSD bond angle	0.969
Data reduction software	XDS
Data scaling software	XDS
Phasing software	PHASER
Refinement software	PHENIX (1.20.1_4487)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	49.850	2.680
High resolution limit [Å]	2.600	2.600
Rpim	0.047	0.326
Number of reflections	52086	4421
<I/σ(I)>	15.9	2.1
Completeness [%]	99.6	99.2
Redundancy	12.9	13.9
CC(1/2)	0.998	0.762

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		295	apoenzyme: 0.12 mM protein, 2.1 M ammonium sulfate, 0.2 M lithium sulfate soak: 2.1 M ammonium sulfate, 0.2 M lithium sulfate, 10 mM NiCl2, 10 mM GTP soak duration: 60 min cryoprotectant: 2.0 M ammonium sulfate, 0.2 M lithium sulfate, 5 mM NiCl2, 5 mM GTP, 20 %(w/v) sucrose