Experiment: 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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	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	0.1882	0.2366	0.2321

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