5EYW

Crystal structure of Litopenaeus vannamei triosephosphate isomerase complexed with 2-Phosphoglycolic acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2I9E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	296	Crystallization experiments was performed with the addition of 15 mM PGA to the concentrated LvTIM protein. Needle-like crystals appeared in a reservoir solution containing 100mM Tris HCl pH 8.5, 30% w/v Polyethylene glycol 4,000 and 200mM Lithium sulfate monohydrate. Protein crystals grew for one week reaching dimensions of 400 x 50 x 50 um.

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.14	α = 74.56
b = 45.98	β = 80.24
c = 71.85	γ = 75.17

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	ADSC QUANTUM 270	1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSING	2013-04-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	0.9795	NSLS	X6A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	1.7	27.15	96.6	0.085	0.099	15.67	5.3		48059			6.6

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	1.7	1.8	93.5		0.314	5.46	5.3

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2I9E	1.7	27.15	1.99	48043	2418	96.6	0.1942	0.192	0.2366

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]
-0.6148	-0.9237	-0.8875	2.0741	-0.18	-1.4592

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.082
f_angle_d	1.089
f_chiral_restr	0.07
f_bond_d	0.007
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3726
Nucleic Acid Atoms
Solvent Atoms	919
Heterogen Atoms	18

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
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 R01GM133198.