5I1F | pdb_00005i1f

Crystal structure of UTP-glucose-1-phosphate uridylyltransferase from Burkholderia vietnamiensis in complex with Uridine-5'-diphosphate-glucose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2UX8	2ux8, chain A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	290	MCSG1 screen A4: 2500mM NaCl, 200mM MgCl2, 100mM Tris base/HCl pH 7.0; BuviA.00118.e.B1.PS02498 at 27.5mg/ml + 4mM Glucose-1-phosphate + 4mM UTP + 4mM MgCl2; ; tray: 267283a4, puck sbq8-1, cryo: 20% EG

Crystal Properties
Matthews coefficient	Solvent content
3.92	68.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.9	α = 90
b = 84.9	β = 90
c = 252.7	γ = 120

Symmetry
Space Group	P 62 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	CCD	RAYONIX MX-225		2015-12-10	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)	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	2.15	50	99.9	0.09	0.998	12.87	6.8		30405		-3	33.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.21	100		0.542	3.56	7.3

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	FREE R-VALUE	2ux8, chain A	2.15	50	1.35	30327	1968	99.9	0.1741	0.172	0.17	0.2025	0.2	45.623

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	17.11
f_angle_d	0.889
f_chiral_restr	0.057
f_bond_d	0.007
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2233
Nucleic Acid Atoms
Solvent Atoms	176
Heterogen Atoms	44

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	model building
PHENIX	refinement