8OOO

Glutamine synthetase from Methanothermococcus thermolithotrophicus in complex with 2-oxoglutarate and MgATP at 2.15 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8OOL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.6	293.15	The enzyme was crystallized at 3.7 mg/ml with a final concentration of 2 mM sodium 2-oxoglutarate, 2 mM ATP and 2 mM MgCl in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol, 150 mM NaCl, 2 mM dithiothreitol. The protein was crystallized fresh without any freezing step, and crystallization was performed through the sitting drop method on a 96-Well MRC 2-Drop Crystallization Plates in polystyrene (SWISSCI, United Kingdom) under anaerobic conditions (N2:H2, gas ratio of 97:3). The crystallization reservoir contained 90 ul of mother liquor (20 % w/v polyethylene glycol 3,350 and 200 mM sodium fluoride). The crystallization drop contained 0.6 ul protein with ligands and 0.6 ul precipitant. Crystals were soaked in the mother liquor supplemented with 20 % v/v glycerol prior to freezing in liquid nitrogen.

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.337	α = 60.04
b = 131.773	β = 87.72
c = 131.507	γ = 67.34

Symmetry
Space Group	P 1

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 PILATUS 2M-F		2020-08-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.30511	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	2.148	110.034	92.2	0.11	0.13	0.068	0.995	9.3	3.6		248419			35.99

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	2.148	2.297	58.8		0.95	1.122	0.59	0.569	1.3	3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	2.149	42.88	248376	12081	77	0.1832	0.1816	0.214	38.36

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]
-0.6437	-0.219	-0.5019	0.383	0.1911	0.2608

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	16.88
t_omega_torsion	3.73
t_angle_deg	0.93
t_bond_d	0.009
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	42408
Nucleic Acid Atoms
Solvent Atoms	3041
Heterogen Atoms	710

Software

Software
Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
STARANISO	data scaling
PHASER	phasing