8OON | pdb_00008oon

Glutamine synthetase from Methanothermococcus thermolithotrophicus at a resolution of 2.43 A

X-RAY DIFFRACTION

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	Protein was crystallized fresh without any freezing step by using 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 enzyme was crystallized at 15 mg/ml in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol, 150 mM NaCl, and 2 mM dithiothreitol. The crystallization reservoir contained 90 uL of mother liquor (20 % w/v polyethylene glycol 3,350 and 100 mM potassium sodium tartrate), the crystallization drop contained a mixture of 0.55 uL protein and 0.55 uL mother liquor. Crystals were soaked in the mother liquor supplemented with 25% v/v ethylene glycol prior to freezing in liquid nitrogen.

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.647	α = 90
b = 230.244	β = 90
c = 205.586	γ = 90

Symmetry
Space Group	C 2 2 21

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		2021-09-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.00004	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	2.43	76.675	93.3	0.269	0.279	0.073	0.998	7.4	14.5		102291			41.5

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	2.43	2.567	49.5		1.795	1.855	0.464	0.782	1.5	15.6

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	2.43	58.89	205.88	102286	7869	86.6	0.233	0.2294	0.25	0.2682	0.28	52.65

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	17.066
f_angle_d	0.654
f_chiral_restr	0.046
f_bond_d	0.004
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21048
Nucleic Acid Atoms
Solvent Atoms	293
Heterogen Atoms	154

Software

Software
Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
STARANISO	data scaling
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 R01GM157729.