8A8G | pdb_00008a8g

ATP sulfurylase from Methanothermococcus thermolithotrophicus - orthorhombic form

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1V47

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	Purified ATPS sulfurylase from Methanothermococcus thermolithotrophicus was concentrated to 14 mg.ml-1 in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol, 2 mM dithiothreitol, and 150 mM NaCl. Crystals were obtained by mixing 0.7 ul of the sample with 0.7 ul of 35 % w/v Pentaerythritol ethoxylate (15/4 EO/OH), and 100 mM 2-(N-morpholino)ethanesulfonic acid (MES) pH 6.5 in a 96-Well MRC 2-drop crystallization plates in polystyrene (SWISSCI) containing 90 ul of crystallization solution in the reservoir.

Crystal Properties
Matthews coefficient	Solvent content
3.8	67.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.705	α = 90
b = 154.457	β = 90
c = 157.575	γ = 90

Symmetry
Space Group	I 2 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	PIXEL	DECTRIS EIGER X 16M		2019-02-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	1.00000	SOLEIL	PROXIMA 1

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	1.97	78.79	93.2	0.151	0.157	0.042	0.998	12.7	13.7		28197			37.7

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	1.97	2.22	62.3		1.74	1.806	0.483	0.641	1.6	13.9

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1V47	1.97	49.73	1.34	28185	1425	58.17	0.19	0.1885	0.19	0.2179	0.21	42.81

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	3136
Nucleic Acid Atoms
Solvent Atoms	208
Heterogen Atoms	49

Software

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