7P50

GlnK2 from Methanothermococcus thermolithotrophicus in complex with Mg-ATP and 2-oxoglutarate at a resolution of 1.16 A

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2J9D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291.15	MtGlnK2 was crystallized at a concentration of 30 mg/ml in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol, 2 mM dithiothreitol and 500 mM NaCl. The protein was co-crystallized with 2 mM ATP, 2 mM 2-oxoglutarate and 2 mM MgCl2 on a 96-Well MRC 2-Drop Crystallization Plates in polystyrene (SWISSCI). Drop of 0.6 ul of protein sample was mixed with 0.6 ul of the crystallization solution. The reservoir contained 90 ul of the following crystallization solution: 25 w/v Pentaerythritol ethoxylate (3/4 EO/OH), 100 mM MES pH 6.5.

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.238	α = 90
b = 58.238	β = 90
c = 229.304	γ = 90

Symmetry
Space Group	P 43 21 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	PIXEL	DECTRIS EIGER2 X 16M		2020-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.99985	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.157	57.33	93.2	0.049	0.05	0.01	0.999	29.1	21.6		108153

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.157	1.259	51.7		0.643	0.709	0.286	0.774	1.7	5.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	THROUGHOUT	2J9D	1.16	57.33	1.35	108153	5309	77.8	0.1178	0.1168	0.1366	20.8654

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2748
Nucleic Acid Atoms
Solvent Atoms	516
Heterogen Atoms	145

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
autoPROC	data reduction
autoPROC	data scaling
MOLREP	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 R01GM157729.