8OOX | pdb_00008oox

Glutamine synthetase from Methermicoccus shengliensis at a resolution of 3.09 A

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.6	293.15	The protein was crystallized fresh without any freezing step, and obtained 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). Crystallization was performed at 9 mg/ml glutamine synthetase in 25 mM Tris/HCl pH 7.6, 10% glycerol, and 2 mM dithiothreitol. The reservoir contained 90 ul precipitant (1.6 M sodium citrate tribasic dihydrate). 0.55 uL protein was mixed with 0.55 uL precipitant. Crystals were soaked in the precipitant supplemented with 30% v/v glycerol before freezing in liquid nitrogen.

Crystal Properties
Matthews coefficient	Solvent content
4.89	74.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 226.465	α = 90
b = 226.465	β = 90
c = 226.465	γ = 90

Symmetry
Space Group	P 43 3 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 PILATUS 2M-F		2021-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.00002	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	3.088	130.75	96.6	0.345	0.352	0.068	0.998	12.2	26.6		35711			83.1

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	3.088	3.172	63.8		3.099	3.159	0.607	0.486	1.4	26.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3.09	65.37	1.34	35696	1748	96.57	0.1878	0.1863	0.185	0.2162	0.2118

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	16.18
f_angle_d	0.678
f_chiral_restr	0.045
f_plane_restr	0.013
f_bond_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6920
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	64

Software

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