6UPE | pdb_00006upe

Structure of trehalose-6-phosphate phosphatase from Salmonella typhimurium inhibited by 4-n-octylphenyl alpha-D-glucopyranoside-6-sulfate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6UPB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		290	Drop contained: 1.5 uL 40 mg/mL protein, 2 uL reservoir solution (15% PEG 3350, 400 mM lithium citrate, 30 mM magnesium chloride, 40 mM mixture of MES, MOPS, and TAPS at pH 7.5), and 0.5 uL 1:10^3 dilution of seed stock prepared according to Seed Bead protocol. Crystals were transferred to drop containing 18% PEG 3350, 400mM lithium citrate, 40 mM magnesium chloride, 10% ethylene glycol, and 1mM OGS for 24 prior to cryocooling

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.159	α = 90
b = 52.419	β = 100.58
c = 108.615	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	290	CCD	MARMOSAIC 325 mm CCD		2016-05-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL14-1	1.378	SSRL	BL14-1

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	2.24	50	99.3	0.107	0.123	0.06	0.978	9.3	4		24547			37.51

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	2.24	2.28	90.6		0.422	0.505	0.273	0.84		3.1

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	6UPB	2.244	37.402	1.35	24528	2009	99.28	0.19	0.1862	0.19	0.232	0.23	43.978

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	3772
Nucleic Acid Atoms
Solvent Atoms	172
Heterogen Atoms	62

Software

Software
Software Name	Purpose
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

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.