6VTJ | pdb_00006vtj

Structure of a thiolation-reductase di-domain from an archaeal non-ribosomal peptide synthetase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4F6C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.1	293.15	Crystals were grown by vapor diffusion, sitting drop method. Drop volume was 2 micro-liter (1+1) equilibrated against 50 micro-liter of reservoir volume of 1.7 M malic acid at pH 6.1. The concentration of protein was 30 mg/ml in HEPES buffer at pH 7.5 containing 150 mM of NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.949	α = 90
b = 71.833	β = 90.26
c = 82.725	γ = 90

Symmetry
Space Group	C 1 2 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 EIGER X 16M		2018-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.948	47.636	92.4	0.993	5.48	3.82		40262			32.22

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.07			0.126

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-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4F6C	1.95	47.62	1.33	39055	1927	91.9	0.198	0.196	0.239	37.17

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	3715
Nucleic Acid Atoms
Solvent Atoms	248
Heterogen Atoms	18

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
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.