5V0T

Crystal structure of an alpha,alpha-trehalose-phosphate synthase (UDP-forming) from Burkholderia xenovorans in complex with glucose-6-phosphate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4B14

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	290	MORPHEUS G2 (269140g2): 10% w/v PEG8000, 20% v/v EG, 20mM tartarate, citrate, oxamate, acetate, formate, 100mM MES/imidazole pH 6.5: 2mM UDP, 2mM glucose-6-phosphate, 2mM MgCl2: protein conc 22.24mg/mL: dc: wpj5-2

Crystal Properties
Matthews coefficient	Solvent content
2.77	56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.92	α = 91.36
b = 105.95	β = 90.37
c = 135.71	γ = 89.97

Symmetry
Space Group	P 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	CCD	RAYONIX MX-225		2016-02-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.95	50	95.7	0.05	0.071	0.997	11.68	1.994		329972		-3	24.74

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2	95.3		0.422	0.597	0.713	1.95	1.995

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4b14	1.95	50	1.97	329927	1982	95.69	0.1555	0.1554	0.1777	32.7772

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	16.137
f_angle_d	0.856
f_chiral_restr	0.053
f_bond_d	0.007
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	28448
Nucleic Acid Atoms
Solvent Atoms	2866
Heterogen Atoms	575

Software

Software
Software Name	Purpose
XSCALE	data scaling
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	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.