6BWR

LarC2, the C-terminal domain of a cyclometallase involved in the synthesis of the NPN cofactor of lactate racemase, in complex with nickel

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 21-ID-D
Synchrotron site	APS
Beamline	21-ID-D
Temperature [K]	100
Detector technology	PIXEL
Collection date	2017-11-20
Detector	DECTRIS EIGER X 9M
Wavelength(s)	1.033
Spacegroup name	P 21 3
Unit cell lengths	96.634, 96.634, 96.634
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	48.317 - 1.810
R-factor	0.1616
Rwork	0.138
R-free	0.19190
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6bwo
RMSD bond length	0.009
RMSD bond angle	0.937
Data reduction software	XDS (2.99)
Data scaling software	Aimless (0.5.32)
Phasing software	PHASER (2.8.0)
Refinement software	PHENIX (1.12-2829)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	48.320	48.320	1.850
High resolution limit [Å]	1.810	9.050	1.810
Rmerge	0.079	0.030	1.109
Rmeas	0.083	0.032	1.174
Rpim	0.027	0.011	0.380
Total number of observations	260115
Number of reflections	27744	257	1665
<I/σ(I)>	19.4
Completeness [%]	99.9	98.4	99.7
Redundancy	9.4	7.9	9.4
CC(1/2)	0.999	0.999	0.537

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	8	294.15	0.5 ul ~5.5 mg/ml LarC (100 mM Tris-HCl pH 7.5, 300 mM NaCl) were mixed with 0.5 ul of reservoir solution. Hanging drop reservoir contained 100 ul of 0.2 M Lithium chloride, 0.1 M Tris pH 8.0, 20% w/v Polyethylene glycol 6,000. Crystal grew within two weeks. The crystal was soaked in 16 mM Nickel chloride + reservoir solution for 30 minutes and then for 1 minute in 20% Polyethylene glycol 400, 80% reservoir solution.