5UDR

LarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase in complex with nicotinamide mononucleotid NMN

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	294.15	5 ul 23 mg/ml LarE (100 mM Tris-HCl pH 7.5, 300 mM NaCl) was mixed with 5 ul of reservoir solution. Hanging drop reservoir contained 100 ul of 30.0% v/v pentaerythritol ethoxylate (15/4 EO/OH), 50 mM BIS-TRIS pH 6.5, 150 mM ammonium sulfate. Crystals grew to full size within 4 days and remained in the drop for 4 months without notable changes. A single crystal was then transfered to a 10 ul drop containing ~100 mM beta-nicotinamide mononucleotide, 30.0% v/v pentaerythritol ethoxylate (15/4 EO/OH) and 50 mM BIS-TRIS pH 6.5. The drop was incubated for 11 days over a hanging drop reservoir containing 100 ul of 30.0% v/v pentaerythritol ethoxylate (15/4 EO/OH), 50 mM BIS-TRIS pH 6.5, 100 mM ammonium sulfate before being directly frozen.

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.095	α = 90
b = 108.095	β = 90
c = 324.964	γ = 90

Symmetry
Space Group	P 41 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD		2016-11-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.9786	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.62	48.42	99.9	0.098	0.999	21.3	12.2		59143			58.05

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.62	2.69	99		1.286	0.72		12.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.62	48.42	1.92	110671	5358	99.87	0.217	0.2155	0.2465	61.9946

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.944
f_angle_d	0.733
f_chiral_restr	0.049
f_bond_d	0.006
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11121
Nucleic Acid Atoms
Solvent Atoms	136
Heterogen Atoms	134

Software

Software
Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.